arXiv subjects

Gregory Slabaugh

Publications and source records attributed to Gregory Slabaugh.

At least 37 records · Page 2Linked to original sources

arXiv2024

Multimodal Outer Arithmetic Block Dual Fusion of Whole Slide Images and Omics Data for Precision Oncology

The integration of DNA methylation data with a Whole Slide Image (WSI) offers significant potential for enhancing the diagnostic precision of central nervous system (CNS) tumor classification in neuropathology. While existing approaches typically integrate encoded omic data with histology at either an early or late fusion stage, the potential of reintroducing omic data through dual fusion remains unexplored. In this paper, we propose the use of omic embeddings during early and late fusion to capture complementary information from local (patch-level) to global (slide-level) interactions, boosting performance through multimodal integration. In the early fusion stage, omic embeddings are projected onto WSI patches in latent-space, which generates embeddings that encapsulate per-patch molecular and morphological insights. This effectively incorporates omic information into the spatial representation of the WSI. These embeddings are then refined with a Multiple Instance Learning gated attention mechanism which attends to diagnostic patches. In the late fusion stage, we reintroduce the omic data by fusing it with slide-level omic-WSI embeddings using a Multimodal Outer Arithmetic Block (MOAB), which richly intermingles features from both modalities, capturing their correlations and complementarity. We demonstrate accurate CNS tumor subtyping across 20 fine-grained subtypes and validate our approach on benchmark datasets, achieving improved survival prediction on TCGA-BLCA and competitive performance on TCGA-BRCA compared to state-of-the-art methods. This dual fusion strategy enhances interpretability and classification performance, highlighting its potential for clinical diagnostics.

cs.CV↗

arXiv2024

Compositional Segmentation of Cardiac Images Leveraging Metadata

Cardiac image segmentation is essential for automated cardiac function assessment and monitoring of changes in cardiac structures over time. Inspired by coarse-to-fine approaches in image analysis, we propose a novel multitask compositional segmentation approach that can simultaneously localize the heart in a cardiac image and perform part-based segmentation of different regions of interest. We demonstrate that this compositional approach achieves better results than direct segmentation of the anatomies. Further, we propose a novel Cross-Modal Feature Integration (CMFI) module to leverage the metadata related to cardiac imaging collected during image acquisition. We perform experiments on two different modalities, MRI and ultrasound, using public datasets, Multi-disease, Multi-View, and Multi-Centre (M&Ms-2) and Multi-structure Ultrasound Segmentation (CAMUS) data, to showcase the efficiency of the proposed compositional segmentation method and Cross-Modal Feature Integration module incorporating metadata within the proposed compositional segmentation network. The source code is available: https://github.com/kabbas570/CompSeg-MetaData.

eess.IV↗

arXiv2024

CAMS: Convolution and Attention-Free Mamba-based Cardiac Image Segmentation

Convolutional Neural Networks (CNNs) and Transformer-based self-attention models have become the standard for medical image segmentation. This paper demonstrates that convolution and self-attention, while widely used, are not the only effective methods for segmentation. Breaking with convention, we present a Convolution and self-Attention-free Mamba-based semantic Segmentation Network named CAMS-Net. Specifically, we design Mamba-based Channel Aggregator and Spatial Aggregator, which are applied independently in each encoder-decoder stage. The Channel Aggregator extracts information across different channels, and the Spatial Aggregator learns features across different spatial locations. We also propose a Linearly Interconnected Factorized Mamba (LIFM) block to reduce the computational complexity of a Mamba block and to enhance its decision function by introducing a non-linearity between two factorized Mamba blocks. Our model outperforms the existing state-of-the-art CNN, self-attention, and Mamba-based methods on CMR and M&Ms-2 Cardiac segmentation datasets, showing how this innovative, convolution, and self-attention-free method can inspire further research beyond CNN and Transformer paradigms, achieving linear complexity and reducing the number of parameters. Source code and pre-trained models are available at: https://github.com/kabbas570/CAMS-Net.

cs.CV↗

arXiv2024

Going Beyond H&E and Oncology: How Do Histopathology Foundation Models Perform for Multi-stain IHC and Immunology?

This study evaluates the generalisation capabilities of state-of-the-art histopathology foundation models on out-of-distribution multi-stain autoimmune Immunohistochemistry datasets. We compare 13 feature extractor models, including ImageNet-pretrained networks, and histopathology foundation models trained on both public and proprietary data, on Rheumatoid Arthritis subtyping and Sjogren's Disease detection tasks. Using a simple Attention-Based Multiple Instance Learning classifier, we assess the transferability of learned representations from cancer H&E images to autoimmune IHC images. Contrary to expectations, histopathology-pretrained models did not significantly outperform ImageNet-pretrained models. Furthermore, there was evidence of both autoimmune feature misinterpretation and biased feature importance. Our findings highlight the challenges in transferring knowledge from cancer to autoimmune histopathology and emphasise the need for careful evaluation of AI models across diverse histopathological tasks. The code to run this benchmark is available at https://github.com/AmayaGS/ImmunoHistoBench.

cs.CV↗

arXiv2024

Adaptive Multi-Modal Control of Digital Human Hand Synthesis Using a Region-Aware Cycle Loss

Diffusion models have shown their remarkable ability to synthesize images, including the generation of humans in specific poses. However, current models face challenges in adequately expressing conditional control for detailed hand pose generation, leading to significant distortion in the hand regions. To tackle this problem, we first curate the How2Sign dataset to provide richer and more accurate hand pose annotations. In addition, we introduce adaptive, multi-modal fusion to integrate characters' physical features expressed in different modalities such as skeleton, depth, and surface normal. Furthermore, we propose a novel Region-Aware Cycle Loss (RACL) that enables the diffusion model training to focus on improving the hand region, resulting in improved quality of generated hand gestures. More specifically, the proposed RACL computes a weighted keypoint distance between the full-body pose keypoints from the generated image and the ground truth, to generate higher-quality hand poses while balancing overall pose accuracy. Moreover, we use two hand region metrics, named hand-PSNR and hand-Distance for hand pose generation evaluations. Our experimental evaluations demonstrate the effectiveness of our proposed approach in improving the quality of digital human pose generation using diffusion models, especially the quality of the hand region. The source code is available at https://github.com/fuqifan/Region-Aware-Cycle-Loss.

cs.CV↗

arXiv2024

RoGUENeRF: A Robust Geometry-Consistent Universal Enhancer for NeRF

Recent advances in neural rendering have enabled highly photorealistic 3D scene reconstruction and novel view synthesis. Despite this progress, current state-of-the-art methods struggle to reconstruct high frequency detail, due to factors such as a low-frequency bias of radiance fields and inaccurate camera calibration. One approach to mitigate this issue is to enhance images post-rendering. 2D enhancers can be pre-trained to recover some detail but are agnostic to scene geometry and do not easily generalize to new distributions of image degradation. Conversely, existing 3D enhancers are able to transfer detail from nearby training images in a generalizable manner, but suffer from inaccurate camera calibration and can propagate errors from the geometry into rendered images. We propose a neural rendering enhancer, RoGUENeRF, which exploits the best of both paradigms. Our method is pre-trained to learn a general enhancer while also leveraging information from nearby training images via robust 3D alignment and geometry-aware fusion. Our approach restores high-frequency textures while maintaining geometric consistency and is also robust to inaccurate camera calibration. We show that RoGUENeRF substantially enhances the rendering quality of a wide range of neural rendering baselines, e.g. improving the PSNR of MipNeRF360 by 0.63dB and Nerfacto by 1.34dB on the real world 360v2 dataset.

cs.CV↗

arXiv2024

RAVE: Residual Vector Embedding for CLIP-Guided Backlit Image Enhancement

In this paper we propose a novel modification of Contrastive Language-Image Pre-Training (CLIP) guidance for the task of unsupervised backlit image enhancement. Our work builds on the state-of-the-art CLIP-LIT approach, which learns a prompt pair by constraining the text-image similarity between a prompt (negative/positive sample) and a corresponding image (backlit image/well-lit image) in the CLIP embedding space. Learned prompts then guide an image enhancement network. Based on the CLIP-LIT framework, we propose two novel methods for CLIP guidance. First, we show that instead of tuning prompts in the space of text embeddings, it is possible to directly tune their embeddings in the latent space without any loss in quality. This accelerates training and potentially enables the use of additional encoders that do not have a text encoder. Second, we propose a novel approach that does not require any prompt tuning. Instead, based on CLIP embeddings of backlit and well-lit images from training data, we compute the residual vector in the embedding space as a simple difference between the mean embeddings of the well-lit and backlit images. This vector then guides the enhancement network during training, pushing a backlit image towards the space of well-lit images. This approach further dramatically reduces training time, stabilizes training and produces high quality enhanced images without artifacts, both in supervised and unsupervised training regimes. Additionally, we show that residual vectors can be interpreted, revealing biases in training data, and thereby enabling potential bias correction.

cs.CV↗

arXiv2024

Improving Interpretability and Robustness for the Detection of AI-Generated Images

With growing abilities of generative models, artificial content detection becomes an increasingly important and difficult task. However, all popular approaches to this problem suffer from poor generalization across domains and generative models. In this work, we focus on the robustness of AI-generated image (AIGI) detectors. We analyze existing state-of-the-art AIGI detection methods based on frozen CLIP embeddings and show how to interpret them, shedding light on how images produced by various AI generators differ from real ones. Next we propose two ways to improve robustness: based on removing harmful components of the embedding vector and based on selecting the best performing attention heads in the image encoder model. Our methods increase the mean out-of-distribution (OOD) classification score by up to 6% for cross-model transfer. We also propose a new dataset for AIGI detection and use it in our evaluation; we believe this dataset will help boost further research. The dataset and code are provided as a supplement.

cs.CV↗

arXiv2024

CUE-Net: Violence Detection Video Analytics with Spatial Cropping, Enhanced UniformerV2 and Modified Efficient Additive Attention

In this paper we introduce CUE-Net, a novel architecture designed for automated violence detection in video surveillance. As surveillance systems become more prevalent due to technological advances and decreasing costs, the challenge of efficiently monitoring vast amounts of video data has intensified. CUE-Net addresses this challenge by combining spatial Cropping with an enhanced version of the UniformerV2 architecture, integrating convolutional and self-attention mechanisms alongside a novel Modified Efficient Additive Attention mechanism (which reduces the quadratic time complexity of self-attention) to effectively and efficiently identify violent activities. This approach aims to overcome traditional challenges such as capturing distant or partially obscured subjects within video frames. By focusing on both local and global spatiotemporal features, CUE-Net achieves state-of-the-art performance on the RWF-2000 and RLVS datasets, surpassing existing methods.

cs.CV↗

arXiv2024

Multi-view Cardiac Image Segmentation via Trans-Dimensional Priors

We propose a novel multi-stage trans-dimensional architecture for multi-view cardiac image segmentation. Our method exploits the relationship between long-axis (2D) and short-axis (3D) magnetic resonance (MR) images to perform a sequential 3D-to-2D-to-3D segmentation, segmenting the long-axis and short-axis images. In the first stage, 3D segmentation is performed using the short-axis image, and the prediction is transformed to the long-axis view and used as a segmentation prior in the next stage. In the second step, the heart region is localized and cropped around the segmentation prior using a Heart Localization and Cropping (HLC) module, focusing the subsequent model on the heart region of the image, where a 2D segmentation is performed. Similarly, we transform the long-axis prediction to the short-axis view, localize and crop the heart region and again perform a 3D segmentation to refine the initial short-axis segmentation. We evaluate our proposed method on the Multi-Disease, Multi-View & Multi-Center Right Ventricular Segmentation in Cardiac MRI (M&Ms-2) dataset, where our method outperforms state-of-the-art methods in segmenting cardiac regions of interest in both short-axis and long-axis images. The pre-trained models, source code, and implementation details will be publicly available.

eess.IV↗

arXiv2024

Graph Neural Networks in Vision-Language Image Understanding: A Survey

2D image understanding is a complex problem within computer vision, but it holds the key to providing human-level scene comprehension. It goes further than identifying the objects in an image, and instead, it attempts to understand the scene. Solutions to this problem form the underpinning of a range of tasks, including image captioning, visual question answering (VQA), and image retrieval. Graphs provide a natural way to represent the relational arrangement between objects in an image, and thus, in recent years graph neural networks (GNNs) have become a standard component of many 2D image understanding pipelines, becoming a core architectural component, especially in the VQA group of tasks. In this survey, we review this rapidly evolving field and we provide a taxonomy of graph types used in 2D image understanding approaches, a comprehensive list of the GNN models used in this domain, and a roadmap of future potential developments. To the best of our knowledge, this is the first comprehensive survey that covers image captioning, visual question answering, and image retrieval techniques that focus on using GNNs as the main part of their architecture.

cs.CV↗

arXiv2024

Machine Learning Techniques for Source Localisation in Elastic Media

Coronary Artery Disease (CAD) results from plaque deposit in a coronary artery. Early diagnosis is imperative, so a non-invasive detection method is being developed to identify acoustic signals caused by partial occlusions in the artery. The blood flow in the artery is disturbed and imposes oscillatory stresses on the artery wall. The deformations caused by the stresses can be detected at the chest surface. Therefore, by using data simulating these surface signals, which arise from randomly assigned source positions, machine learning (ML) can be utilised to predict the source of the occlusion. Seven ML algorithms were investigated, and the results from this study found that an ensemble model combining k-Nearest Neighbours and Random Forest had the best performance. The metrics used to evaluate this was the mean squared error and Euclidean distance.

eess.SP↗

arXiv2024

MOAB: Multi-Modal Outer Arithmetic Block For Fusion Of Histopathological Images And Genetic Data For Brain Tumor Grading

Brain tumors are an abnormal growth of cells in the brain. They can be classified into distinct grades based on their growth. Often grading is performed based on a histological image and is one of the most significant predictors of a patients prognosis, the higher the grade, the more aggressive the tumor. Correct diagnosis of a tumor grade remains challenging. Though histopathological grading has been shown to be prognostic, results are subject to interobserver variability, even among experienced pathologists. Recently, the World Health Organization reported that advances in molecular genetics have led to improvements in tumor classification. This paper seeks to integrate histological images and genetic data for improved computer-aided diagnosis. We propose a novel Multi-modal Outer Arithmetic Block (MOAB) based on arithmetic operations to combine latent representations of the different modalities for predicting the tumor grade (Grade \rom{2}, \rom{3} and \rom{4}). Extensive experiments evaluate the effectiveness of our approach. By applying MOAB to The Cancer Genome Atlas (TCGA) glioma dataset, we show that it can improve separation between similar classes (Grade \rom{2} and \rom{3}) and outperform prior state-of-the-art grade classification techniques.

cs.CV↗

arXiv2024

FOAA: Flattened Outer Arithmetic Attention For Multimodal Tumor Classification

Fusion of multimodal healthcare data holds great promise to provide a holistic view of a patient's health, taking advantage of the complementarity of different modalities while leveraging their correlation. This paper proposes a simple and effective approach, inspired by attention, to fuse discriminative features from different modalities. We propose a novel attention mechanism, called Flattened Outer Arithmetic Attention (FOAA), which relies on outer arithmetic operators (addition, subtraction, product, and division) to compute attention scores from keys, queries and values derived from flattened embeddings of each modality. We demonstrate how FOAA can be implemented for self-attention and cross-attention, providing a reusable component in neural network architectures. We evaluate FOAA on two datasets for multimodal tumor classification and achieve state-of-the-art results, and we demonstrate that features enriched by FOAA are superior to those derived from other fusion approaches. The code is publicly available at \href{https://github.com/omniaalwazzan/FOAA}{https://github.com/omniaalwazzan/FOAA}

cs.CV↗

arXiv2024

Crop and Couple: cardiac image segmentation using interlinked specialist networks

Diagnosis of cardiovascular disease using automated methods often relies on the critical task of cardiac image segmentation. We propose a novel strategy that performs segmentation using specialist networks that focus on a single anatomy (left ventricle, right ventricle, or myocardium). Given an input long-axis cardiac MR image, our method performs a ternary segmentation in the first stage to identify these anatomical regions, followed by cropping the original image to focus subsequent processing on the anatomical regions. The specialist networks are coupled through an attention mechanism that performs cross-attention to interlink features from different anatomies, serving as a soft relative shape prior. Central to our approach is an additive attention block (E-2A block), which is used throughout our architecture thanks to its efficiency.

eess.IV↗

arXiv2023

MUSTANG: Multi-Stain Self-Attention Graph Multiple Instance Learning Pipeline for Histopathology Whole Slide Images

Whole Slide Images (WSIs) present a challenging computer vision task due to their gigapixel size and presence of numerous artefacts. Yet they are a valuable resource for patient diagnosis and stratification, often representing the gold standard for diagnostic tasks. Real-world clinical datasets tend to come as sets of heterogeneous WSIs with labels present at the patient-level, with poor to no annotations. Weakly supervised attention-based multiple instance learning approaches have been developed in recent years to address these challenges, but can fail to resolve both long and short-range dependencies. Here we propose an end-to-end multi-stain self-attention graph (MUSTANG) multiple instance learning pipeline, which is designed to solve a weakly-supervised gigapixel multi-image classification task, where the label is assigned at the patient-level, but no slide-level labels or region annotations are available. The pipeline uses a self-attention based approach by restricting the operations to a highly sparse k-Nearest Neighbour Graph of embedded WSI patches based on the Euclidean distance. We show this approach achieves a state-of-the-art F1-score/AUC of 0.89/0.92, outperforming the widely used CLAM model. Our approach is highly modular and can easily be modified to suit different clinical datasets, as it only requires a patient-level label without annotations and accepts WSI sets of different sizes, as the graphs can be of varying sizes and structures. The source code can be found at https://github.com/AmayaGS/MUSTANG.

cs.CV↗

arXiv2023

Automated segmentation of rheumatoid arthritis immunohistochemistry stained synovial tissue

Rheumatoid Arthritis (RA) is a chronic, autoimmune disease which primarily affects the joint's synovial tissue. It is a highly heterogeneous disease, with wide cellular and molecular variability observed in synovial tissues. Over the last two decades, the methods available for their study have advanced considerably. In particular, Immunohistochemistry stains are well suited to highlighting the functional organisation of samples. Yet, analysis of IHC-stained synovial tissue samples is still overwhelmingly done manually and semi-quantitatively by expert pathologists. This is because in addition to the fragmented nature of IHC stained synovial tissue, there exist wide variations in intensity and colour, strong clinical centre batch effect, as well as the presence of many undesirable artefacts present in gigapixel Whole Slide Images (WSIs), such as water droplets, pen annotation, folded tissue, blurriness, etc. There is therefore a strong need for a robust, repeatable automated tissue segmentation algorithm which can cope with this variability and provide support to imaging pipelines. We train a UNET on a hand-curated, heterogeneous real-world multi-centre clinical dataset R4RA, which contains multiple types of IHC staining. The model obtains a DICE score of 0.865 and successfully segments different types of IHC staining, as well as dealing with variance in colours, intensity and common WSIs artefacts from the different clinical centres. It can be used as the first step in an automated image analysis pipeline for synovial tissue samples stained with IHC, increasing speed, reproducibility and robustness.

eess.IV↗

arXiv2023

Vector Quantized Semantic Communication System

Although analog semantic communication systems have received considerable attention in the literature, there is less work on digital semantic communication systems. In this paper, we develop a deep learning (DL)-enabled vector quantized (VQ) semantic communication system for image transmission, named VQ-DeepSC. Specifically, we propose a convolutional neural network (CNN)-based transceiver to extract multi-scale semantic features of images and introduce multi-scale semantic embedding spaces to perform semantic feature quantization, rendering the data compatible with digital communication systems. Furthermore, we employ adversarial training to improve the quality of received images by introducing a PatchGAN discriminator. Experimental results demonstrate that the proposed VQ-DeepSC is more robustness than BPG in digital communication systems and has comparable MS-SSIM performance to the DeepJSCC method.

cs.CV↗