Mahdi S. Hosseini

Mahdi S. Hosseini, Babak Ehteshami Bejnordi, Vincent Quoc-Huy Trinh et al.

Computational Pathology CPath is an interdisciplinary science that augments developments of computational approaches to analyze and model medical histopathology images. The main objective for CPath is to develop infrastructure and workflows of digital diagnostics as an assistive CAD system for clinical pathology, facilitating transformational changes in the diagnosis and treatment of cancer that are mainly address by CPath tools. With evergrowing developments in deep learning and computer vision algorithms, and the ease of the data flow from digital pathology, currently CPath is witnessing a paradigm shift. Despite the sheer volume of engineering and scientific works being introduced for cancer image analysis, there is still a considerable gap of adopting and integrating these algorithms in clinical practice. This raises a significant question regarding the direction and trends that are undertaken in CPath. In this article we provide a comprehensive review of more than 800 papers to address the challenges faced in problem design all-the-way to the application and implementation viewpoints. We have catalogued each paper into a model-card by examining the key works and challenges faced to layout the current landscape in CPath. We hope this helps the community to locate relevant works and facilitate understanding of the field's future directions. In a nutshell, we oversee the CPath developments in cycle of stages which are required to be cohesively linked together to address the challenges associated with such multidisciplinary science. We overview this cycle from different perspectives of data-centric, model-centric, and application-centric problems. We finally sketch remaining challenges and provide directions for future technical developments and clinical integration of CPath (https://github.com/AtlasAnalyticsLab/CPath_Survey).

Ahmad Sajedi, Samir Khaki, Konstantinos N. Plataniotis et al.

Multilabel representation learning is recognized as a challenging problem that can be associated with either label dependencies between object categories or data-related issues such as the inherent imbalance of positive/negative samples. Recent advances address these challenges from model- and data-centric viewpoints. In model-centric, the label correlation is obtained by an external model designs (e.g., graph CNN) to incorporate an inductive bias for training. However, they fail to design an end-to-end training framework, leading to high computational complexity. On the contrary, in data-centric, the realistic nature of the dataset is considered for improving the classification while ignoring the label dependencies. In this paper, we propose a new end-to-end training framework -- dubbed KMCL (Kernel-based Mutlilabel Contrastive Learning) -- to address the shortcomings of both model- and data-centric designs. The KMCL first transforms the embedded features into a mixture of exponential kernels in Gaussian RKHS. It is then followed by encoding an objective loss that is comprised of (a) reconstruction loss to reconstruct kernel representation, (b) asymmetric classification loss to address the inherent imbalance problem, and (c) contrastive loss to capture label correlation. The KMCL models the uncertainty of the feature encoder while maintaining a low computational footprint. Extensive experiments are conducted on image classification tasks to showcase the consistent improvements of KMCL over the SOTA methods. PyTorch implementation is provided in \url{https://github.com/mahdihosseini/KMCL}.

Arash Ahmadian, Louis S. P. Liu, Yue Fei et al.

Differentiable Architecture Search (DARTS) has attracted considerable attention as a gradient-based neural architecture search method. Since the introduction of DARTS, there has been little work done on adapting the action space based on state-of-art architecture design principles for CNNs. In this work, we aim to address this gap by incrementally augmenting the DARTS search space with micro-design changes inspired by ConvNeXt and studying the trade-off between accuracy, evaluation layer count, and computational cost. We introduce the Pseudo-Inverted Bottleneck Conv (PIBConv) block intending to reduce the computational footprint of the inverted bottleneck block proposed in ConvNeXt. Our proposed architecture is much less sensitive to evaluation layer count and outperforms a DARTS network with similar size significantly, at layer counts as small as 2. Furthermore, with less layers, not only does it achieve higher accuracy with lower computational footprint (measured in GMACs) and parameter count, GradCAM comparisons show that our network can better detect distinctive features of target objects compared to DARTS. Code is available from https://github.com/mahdihosseini/PIBConv.

Mahdi S. Hosseini, Konstantinos N. Plataniotis

A systematic and comprehensive framework for finite impulse response (FIR) lowpass/fullband derivative kernels is introduced in this paper. Closed form solutions of a number of derivative filters are obtained using the maximally flat technique to regulate the Fourier response of undetermined coefficients. The framework includes arbitrary parameter control methods that afford solutions for numerous differential orders, variable polynomial accuracy, centralized/staggered schemes, and arbitrary side-shift nodes for boundary formulation. Using the proposed framework four different derivative matrix operators are introduced and their numerical stability is analyzed by studying their eigenvalues distribution in the complex plane. Their utility is studied by considering two important image processing problems, namely gradient surface reconstruction and image stitching. Experimentation indicates that the new derivative matrices not only outperform commonly used method but provide useful insights to the numerical issues in these two applications.

Ali Nasiri-Sarvi, Mahdi S. Hosseini, Hassan Rivaz

Mamba-based models, VMamba and Vim, are a recent family of vision encoders that offer promising performance improvements in many computer vision tasks. This paper compares Mamba-based models with traditional Convolutional Neural Networks (CNNs) and Vision Transformers (ViTs) using the breast ultrasound BUSI dataset and Breast Ultrasound B dataset. Our evaluation, which includes multiple runs of experiments and statistical significance analysis, demonstrates that some of the Mamba-based architectures often outperform CNN and ViT models with statistically significant results. For example, in the B dataset, the best Mamba-based models have a 1.98\% average AUC and a 5.0\% average Accuracy improvement compared to the best non-Mamba-based model in this study. These Mamba-based models effectively capture long-range dependencies while maintaining some inductive biases, making them suitable for applications with limited data. The code is available at \url{https://github.com/anasiri/BU-Mamba}

Ali Nasiri-Sarvi, Vincent Quoc-Huy Trinh, Hassan Rivaz et al.

Representation learning from Gigapixel Whole Slide Images (WSI) poses a significant challenge in computational pathology due to the complicated nature of tissue structures and the scarcity of labeled data. Multi-instance learning methods have addressed this challenge, leveraging image patches to classify slides utilizing pretrained models using Self-Supervised Learning (SSL) approaches. The performance of both SSL and MIL methods relies on the architecture of the feature encoder. This paper proposes leveraging the Vision Mamba (Vim) architecture, inspired by state space models, within the DINO framework for representation learning in computational pathology. We evaluate the performance of Vim against Vision Transformers (ViT) on the Camelyon16 dataset for both patch-level and slide-level classification. Our findings highlight Vim's enhanced performance compared to ViT, particularly at smaller scales, where Vim achieves an 8.21 increase in ROC AUC for models of similar size. An explainability analysis further highlights Vim's capabilities, which reveals that Vim uniquely emulates the pathologist workflow-unlike ViT. This alignment with human expert analysis highlights Vim's potential in practical diagnostic settings and contributes significantly to developing effective representation-learning algorithms in computational pathology. We release the codes and pretrained weights at \url{https://github.com/AtlasAnalyticsLab/Vim4Path}.

Jingwei Zhang, Anh Tien Nguyen, Xi Han et al.

Efficiently modeling large 2D contexts is essential for various fields including Giga-Pixel Whole Slide Imaging (WSI) and remote sensing. Transformer-based models offer high parallelism but face challenges due to their quadratic complexity for handling long sequences. Recently, Mamba introduced a selective State Space Model (SSM) with linear complexity and high parallelism, enabling effective and efficient modeling of wide context in 1D sequences. However, extending Mamba to vision tasks, which inherently involve 2D structures, results in spatial discrepancies due to the limitations of 1D sequence processing. On the other hand, current 2D SSMs inherently model 2D structures but they suffer from prohibitively slow computation due to the lack of efficient parallel algorithms. In this work, we propose 2DMamba, a novel 2D selective SSM framework that incorporates the 2D spatial structure of images into Mamba, with a highly optimized hardware-aware operator, adopting both spatial continuity and computational efficiency. We validate the versatility of our approach on both WSIs and natural images. Extensive experiments on 10 public datasets for WSI classification and survival analysis show that 2DMamba improves up to 2.48% in AUC, 3.11% in F1 score, 2.47% in accuracy and 5.52% in C-index. Additionally, integrating our method with VMamba for natural imaging yields 0.5 to 0.7 improvements in mIoU on the ADE20k semantic segmentation dataset, and 0.2% accuracy improvement on ImageNet-1K classification dataset. Our code is available at https://github.com/AtlasAnalyticsLab/2DMamba.

Benoit Freiche, Anthony El-Khoury, Ali Nasiri-Sarvi et al.

Diffusion models for image generation have been a subject of increasing interest due to their ability to generate diverse, high-quality images. Image generation has immense potential in medical imaging because open-source medical images are difficult to obtain compared to natural images, especially for rare conditions. The generated images can be used later to train classification and segmentation models. In this paper, we propose simulating realistic ultrasound (US) images by successive fine-tuning of large diffusion models on different publicly available databases. To do so, we fine-tuned Stable Diffusion, a state-of-the-art latent diffusion model, on BUSI (Breast US Images) an ultrasound breast image dataset. We successfully generated high-quality US images of the breast using simple prompts that specify the organ and pathology, which appeared realistic to three experienced US scientists and a US radiologist. Additionally, we provided user control by conditioning the model with segmentations through ControlNet. We will release the source code at http://code.sonography.ai/ to allow fast US image generation to the scientific community.

Denisha Thakkar, Vincent Quoc-Huy Trinh, Sonal Varma et al.

Diffusion Generative Models (DGM) have rapidly surfaced as emerging topics in the field of computer vision, garnering significant interest across a wide array of deep learning applications. Despite their high computational demand, these models are extensively utilized for their superior sample quality and robust mode coverage. While research in diffusion generative models is advancing, exploration within the domain of computational pathology and its large-scale datasets has been comparatively gradual. Bridging the gap between the high-quality generation capabilities of Diffusion Generative Models and the intricate nature of pathology data, this paper presents an in-depth comparative analysis of diffusion methods applied to a pathology dataset. Our analysis extends to datasets with varying Fields of View (FOV), revealing that DGMs are highly effective in producing high-quality synthetic data. An ablative study is also conducted, followed by a detailed discussion on the impact of various methods on the synthesized histopathology images. One striking observation from our experiments is how the adjustment of image size during data generation can simulate varying fields of view. These findings underscore the potential of DGMs to enhance the quality and diversity of synthetic pathology data, especially when used with real data, ultimately increasing accuracy of deep learning models in histopathology. Code is available from https://github.com/AtlasAnalyticsLab/Diffusion4Path

Ali Nasiri-Sarvi, Hassan Rivaz, Mahdi S. Hosseini

Understanding how different AI models encode the same high-level concepts, such as objects or attributes, remains challenging because each model typically produces its own isolated representation. Existing interpretability methods like Sparse Autoencoders (SAEs) produce latent concepts individually for each model, resulting in incompatible concept spaces and limiting cross-model interpretability. To address this, we introduce SPARC (Sparse Autoencoders for Aligned Representation of Concepts), a new framework that learns a single, unified latent space shared across diverse architectures and modalities (e.g., vision models like DINO, and multimodal models like CLIP). SPARC's alignment is enforced through two key innovations: (1) a Global TopK sparsity mechanism, ensuring all input streams activate identical latent dimensions for a given concept; and (2) a Cross-Reconstruction Loss, which explicitly encourages semantic consistency between models. On Open Images, SPARC dramatically improves concept alignment, achieving a Jaccard similarity of 0.80, more than tripling the alignment compared to previous methods. SPARC creates a shared sparse latent space where individual dimensions often correspond to similar high-level concepts across models and modalities, enabling direct comparison of how different architectures represent identical concepts without requiring manual alignment or model-specific analysis. As a consequence of this aligned representation, SPARC also enables practical applications such as text-guided spatial localization in vision-only models and cross-model/cross-modal retrieval. Code and models are available at https://github.com/AtlasAnalyticsLab/SPARC.

Cassandre Notton, Vasudev Sharma, Vincent Quoc-Huy Trinh et al.

Colorectal cancer (CRC) is one of the few cancers that have an established dysplasia-carcinoma sequence that benefits from screening. Everyone over 50 years of age in Canada is eligible for CRC screening. About 20\% of those people will undergo a biopsy for a pre-neoplastic polyp and, in many cases, multiple polyps. As such, these polyp biopsies make up the bulk of a pathologist's workload. Developing an efficient computational model to help screen these polyp biopsies can improve the pathologist's workflow and help guide their attention to critical areas on the slide. DL models face significant challenges in computational pathology (CPath) because of the gigapixel image size of whole-slide images and the scarcity of detailed annotated datasets. It is, therefore, crucial to leverage self-supervised learning (SSL) methods to alleviate the burden and cost of data annotation. However, current research lacks methods to apply SSL frameworks to analyze pathology data effectively. This paper aims to propose an optimized Barlow Twins framework for colorectal polyps screening. We adapt its hyperparameters, augmentation strategy and encoder to the specificity of the pathology data to enhance performance. Additionally, we investigate the best Field of View (FoV) for colorectal polyps screening and propose a new benchmark dataset for CRC screening, made of four types of colorectal polyps and normal tissue, by performing downstream tasking on MHIST and NCT-CRC-7K datasets. Furthermore, we show that the SSL representations are more meaningful and qualitative than the supervised ones and that Barlow Twins benefits from the Swin Transformer when applied to pathology data. Codes are avaialble from https://github.com/AtlasAnalyticsLab/PathBT.

Mathieu Tuli, Mahdi S. Hosseini, Konstantinos N. Plataniotis

The task of hyper-parameter optimization (HPO) is burdened with heavy computational costs due to the intractability of optimizing both a model's weights and its hyper-parameters simultaneously. In this work, we introduce a new class of HPO method and explore how the low-rank factorization of the convolutional weights of intermediate layers of a convolutional neural network can be used to define an analytical response surface for optimizing hyper-parameters, using only training data. We quantify how this surface behaves as a surrogate to model performance and can be solved using a trust-region search algorithm, which we call autoHyper. The algorithm outperforms state-of-the-art such as Bayesian Optimization and generalizes across model, optimizer, and dataset selection. Our code can be found at \url{https://github.com/MathieuTuli/autoHyper}.

Mahdi S. Hosseini, Konstantinos N. Plataniotis

The choice of step-size used in Stochastic Gradient Descent (SGD) optimization is empirically selected in most training procedures. Moreover, the use of scheduled learning techniques such as Step-Decaying, Cyclical-Learning, and Warmup to tune the step-size requires extensive practical experience--offering limited insight into how the parameters update--and is not consistent across applications. This work attempts to answer a question of interest to both researchers and practitioners, namely \textit{"how much knowledge is gained in iterative training of deep neural networks?"} Answering this question introduces two useful metrics derived from the singular values of the low-rank factorization of convolution layers in deep neural networks. We introduce the notions of \textit{"knowledge gain"} and \textit{"mapping condition"} and propose a new algorithm called Adaptive Scheduling (AdaS) that utilizes these derived metrics to adapt the SGD learning rate proportionally to the rate of change in knowledge gain over successive iterations. Experimentation reveals that, using the derived metrics, AdaS exhibits: (a) faster convergence and superior generalization over existing adaptive learning methods; and (b) lack of dependence on a validation set to determine when to stop training. Code is available at \url{https://github.com/mahdihosseini/AdaS}.

Zhiyuan Yang, Kai Li, Sophia Ghamoshi Ramandi et al.

Computational pathology (CoPath) leverages histopathology images to enhance diagnostic precision and reproducibility in clinical pathology. However, publicly available datasets for CoPath that are annotated with extensive histological tissue type (HTT) taxonomies at a granular level remain scarce due to the significant expertise and high annotation costs required. Existing datasets, such as the Atlas of Digital Pathology (ADP), address this by offering diverse HTT annotations generalized to multiple organs, but limit the capability for in-depth studies on specific organ diseases. Building upon this foundation, we introduce ADPv2, a novel dataset focused on gastrointestinal histopathology. Our dataset comprises 20,004 image patches derived from healthy colon biopsy slides, annotated according to a hierarchical taxonomy of 32 distinct HTTs of 3 levels. Furthermore, we train a multilabel representation learning model following a two-stage training procedure on our ADPv2 dataset. We leverage the VMamba architecture and achieving a mean average precision (mAP) of 0.88 in multilabel classification of colon HTTs. Finally, we show that our dataset is capable of an organ-specific in-depth study for potential biomarker discovery by analyzing the model's prediction behavior on tissues affected by different colon diseases, which reveals statistical patterns that confirm the two pathological pathways of colon cancer development. Our dataset is publicly available at https://zenodo.org/records/15307021

Mahdi S. Hosseini, Mathieu Tuli, Konstantinos N. Plataniotis

Explaining the generalization characteristics of deep learning is an emerging topic in advanced machine learning. There are several unanswered questions about how learning under stochastic optimization really works and why certain strategies are better than others. In this paper, we address the following question: \textit{can we probe intermediate layers of a deep neural network to identify and quantify the learning quality of each layer?} With this question in mind, we propose new explainability metrics that measure the redundant information in a network's layers using a low-rank factorization framework and quantify a complexity measure that is highly correlated with the generalization performance of a given optimizer, network, and dataset. We subsequently exploit these metrics to augment the Stochastic Gradient Descent (SGD) optimizer by adaptively adjusting the learning rate in each layer to improve in generalization performance. Our augmented SGD -- dubbed RMSGD -- introduces minimal computational overhead compared to SOTA methods and outperforms them by exhibiting strong generalization characteristics across application, architecture, and dataset.

Ryan Zhang, Jiadai Zhu, Stephen Yang et al.

The lack of well-annotated datasets in computational pathology (CPath) obstructs the application of deep learning techniques for classifying medical images. %Since pathologist time is expensive, dataset curation is intrinsically difficult. Many CPath workflows involve transferring learned knowledge between various image domains through transfer learning. Currently, most transfer learning research follows a model-centric approach, tuning network parameters to improve transfer results over few datasets. In this paper, we take a data-centric approach to the transfer learning problem and examine the existence of generalizable knowledge between histopathological datasets. First, we create a standardization workflow for aggregating existing histopathological data. We then measure inter-domain knowledge by training ResNet18 models across multiple histopathological datasets, and cross-transferring between them to determine the quantity and quality of innate shared knowledge. Additionally, we use weight distillation to share knowledge between models without additional training. We find that hard to learn, multi-class datasets benefit most from pretraining, and a two stage learning framework incorporating a large source domain such as ImageNet allows for better utilization of smaller datasets. Furthermore, we find that weight distillation enables models trained on purely histopathological features to outperform models using external natural image data.

Andre Fu, Elisa Ding, Mahdi S. Hosseini et al.

The field of computer vision is rapidly evolving, particularly in the context of new methods of neural architecture design. These models contribute to (1) the Climate Crisis - increased CO2 emissions and (2) the Privacy Crisis - data leakage concerns. To address the often overlooked impact the Computer Vision (CV) community has on these crises, we outline a novel ethical framework, \textit{P4AI}: Principlism for AI, an augmented principlistic view of ethical dilemmas within AI. We then suggest using P4AI to make concrete recommendations to the community to mitigate the climate and privacy crises.

Andre Fu, Justin Tran, Andy Xie et al.

Climate change continues to be a pressing issue that currently affects society at-large. It is important that we as a society, including the Computer Vision (CV) community take steps to limit our impact on the environment. In this paper, we (a) analyze the effect of diminishing returns on CV methods, and (b) propose a \textit{``NoFADE''}: a novel entropy-based metric to quantify model--dataset--complexity relationships. We show that some CV tasks are reaching saturation, while others are almost fully saturated. In this light, NoFADE allows the CV community to compare models and datasets on a similar basis, establishing an agnostic platform.

Jonathan Jaegerman, Khalil Damouni, Mahdi S. Hosseini et al.

Understanding the generalization behaviour of deep neural networks is a topic of recent interest that has driven the production of many studies, notably the development and evaluation of generalization "explainability" measures that quantify model generalization ability. Generalization measures have also proven useful in the development of powerful layer-wise model tuning and optimization algorithms, though these algorithms require specific kinds of generalization measures which can probe individual layers. The purpose of this paper is to explore the neglected subtopic of probeable generalization measures; to establish firm ground for further investigations, and to inspire and guide the development of novel model tuning and optimization algorithms. We evaluate and compare measures, demonstrating effectiveness and robustness across model variations, dataset complexities, training hyperparameters, and training stages. We also introduce a new dataset of trained models and performance metrics, GenProb, for testing generalization measures, model tuning algorithms and optimization algorithms.

Yi Ru Wang, Samir Khaki, Weihang Zheng et al.

Neural Architecture Search (NAS) has been pivotal in finding optimal network configurations for Convolution Neural Networks (CNNs). While many methods explore NAS from a global search-space perspective, the employed optimization schemes typically require heavy computational resources. This work introduces a method that is efficient in computationally constrained environments by examining the micro-search space of channel size. In tackling channel-size optimization, we design an automated algorithm to extract the dependencies within different connected layers of the network. In addition, we introduce the idea of knowledge distillation, which enables preservation of trained weights, admist trials where the channel sizes are changing. Further, since the standard performance indicators (accuracy, loss) fail to capture the performance of individual network components (providing an overall network evaluation), we introduce a novel metric that highly correlates with test accuracy and enables analysis of individual network layers. Combining dependency extraction, metrics, and knowledge distillation, we introduce an efficient searching algorithm, with simulated annealing inspired stochasticity, and demonstrate its effectiveness in finding optimal architectures that outperform baselines by a large margin.

Sheyang Tang, Mahdi S. Hosseini, Lina Chen et al.

AI technology has made remarkable achievements in computational pathology (CPath), especially with the help of deep neural networks. However, the network performance is highly related to architecture design, which commonly requires human experts with domain knowledge. In this paper, we combat this challenge with the recent advance in neural architecture search (NAS) to find an optimal network for CPath applications. In particular, we use differentiable architecture search (DARTS) for its efficiency. We first adopt a probing metric to show that the original DARTS lacks proper hyperparameter tuning on the CIFAR dataset, and how the generalization issue can be addressed using an adaptive optimization strategy. We then apply our searching framework on CPath applications by searching for the optimum network architecture on a histological tissue type dataset (ADP). Results show that the searched network outperforms state-of-the-art networks in terms of prediction accuracy and computation complexity. We further conduct extensive experiments to demonstrate the transferability of the searched network to new CPath applications, the robustness against downscaled inputs, as well as the reliability of predictions.

Mahdi S. Hosseini, Jia Shu Zhang, Zhe Liu et al.

Neural Architecture Search (NAS) has shifted network design from using human intuition to leveraging search algorithms guided by evaluation metrics. We study channel size optimization in convolutional neural networks (CNN) and identify the role it plays in model accuracy and complexity. Current channel size selection methods are generally limited by discrete sample spaces while suffering from manual iteration and simple heuristics. To solve this, we introduce an efficient dynamic scaling algorithm -- CONet -- that automatically optimizes channel sizes across network layers for a given CNN. Two metrics -- "\textit{Rank}" and "\textit{Rank Average Slope}" -- are introduced to identify the information accumulated in training. The algorithm dynamically scales channel sizes up or down over a fixed searching phase. We conduct experiments on CIFAR10/100 and ImageNet datasets and show that CONet can find efficient and accurate architectures searched in ResNet, DARTS, and DARTS+ spaces that outperform their baseline models. This document supersedes previously published paper in ICCV2021-NeurArch workshop. An additional section is included on manual scaling of channel size in CNNs to numerically validate of the metrics used in searching optimum channel configurations in CNNs.

Andre Fu, Mahdi S. Hosseini, Konstantinos N. Plataniotis

Climate change is a pressing issue that is currently affecting and will affect every part of our lives. It's becoming incredibly vital we, as a society, address the climate crisis as a universal effort, including those in the Computer Vision (CV) community. In this work, we analyze the total cost of CO2 emissions by breaking it into (1) the architecture creation cost and (2) the life-time evaluation cost. We show that over time, these costs are non-negligible and are having a direct impact on our future. Importantly, we conduct an ethical analysis of how the CV-community is unintentionally overlooking its own ethical AI principles by emitting this level of CO2. To address these concerns, we propose adding "enforcement" as a pillar of ethical AI and provide some recommendations for how architecture designers and broader CV community can curb the climate crisis.

Zhongling Wang, Mahdi S. Hosseini, Adyn Miles et al.

Out-of-focus microscopy lens in digital pathology is a critical bottleneck in high-throughput Whole Slide Image (WSI) scanning platforms, for which pixel-level automated Focus Quality Assessment (FQA) methods are highly desirable to help significantly accelerate the clinical workflows. Existing FQA methods include both knowledge-driven and data-driven approaches. While data-driven approaches such as Convolutional Neural Network (CNN) based methods have shown great promises, they are difficult to use in practice due to their high computational complexity and lack of transferability. Here, we propose a highly efficient CNN-based model that maintains fast computations similar to the knowledge-driven methods without excessive hardware requirements such as GPUs. We create a training dataset using FocusPath which encompasses diverse tissue slides across nine different stain colors, where the stain diversity greatly helps the model to learn diverse color spectrum and tissue structures. In our attempt to reduce the CNN complexity, we find with surprise that even trimming down the CNN to the minimal level, it still achieves a highly competitive performance. We introduce a novel comprehensive evaluation dataset, the largest of its kind, annotated and compiled from TCGA repository for model assessment and comparison, for which the proposed method exhibits superior precision-speed trade-off when compared with existing knowledge-driven and data-driven FQA approaches.

Mahdi S. Hosseini, Yueyang Zhang, Lyndon Chan et al.

One of the challenges facing the adoption of digital pathology workflows for clinical use is the need for automated quality control. As the scanners sometimes determine focus inaccurately, the resultant image blur deteriorates the scanned slide to the point of being unusable. Also, the scanned slide images tend to be extremely large when scanned at greater or equal 20X image resolution. Hence, for digital pathology to be clinically useful, it is necessary to use computational tools to quickly and accurately quantify the image focus quality and determine whether an image needs to be re-scanned. We propose a no-reference focus quality assessment metric specifically for digital pathology images, that operates by using a sum of even-derivative filter bases to synthesize a human visual system-like kernel, which is modeled as the inverse of the lens' point spread function. This kernel is then applied to a digital pathology image to modify high-frequency image information deteriorated by the scanner's optics and quantify the focus quality at the patch level. We show in several experiments that our method correlates better with ground-truth $z$-level data than other methods, and is more computationally efficient. We also extend our method to generate a local slide-level focus quality heatmap, which can be used for automated slide quality control, and demonstrate the utility of our method for clinical scan quality control by comparison with subjective slide quality scores.

Mahdi S. Hosseini, Konstantinos N. Plataniotis

In this paper, we propose a novel design of image deblurring in the form of one-shot convolution filtering that can directly convolve with naturally blurred images for restoration. The problem of optical blurring is a common disadvantage to many imaging applications that suffer from optical imperfections. Despite numerous deconvolution methods that blindly estimate blurring in either inclusive or exclusive forms, they are practically challenging due to high computational cost and low image reconstruction quality. Both conditions of high accuracy and high speed are prerequisites for high-throughput imaging platforms in digital archiving. In such platforms, deblurring is required after image acquisition before being stored, previewed, or processed for high-level interpretation. Therefore, on-the-fly correction of such images is important to avoid possible time delays, mitigate computational expenses, and increase image perception quality. We bridge this gap by synthesizing a deconvolution kernel as a linear combination of Finite Impulse Response (FIR) even-derivative filters that can be directly convolved with blurry input images to boost the frequency fall-off of the Point Spread Function (PSF) associated with the optical blur. We employ a Gaussian low-pass filter to decouple the image denoising problem for image edge deblurring. Furthermore, we propose a blind approach to estimate the PSF statistics for two Gaussian and Laplacian models that are common in many imaging pipelines. Thorough experiments are designed to test and validate the efficiency of the proposed method using 2054 naturally blurred images across six imaging applications and seven state-of-the-art deconvolution methods.