arXiv subjects

Sharib Ali

Publications and source records attributed to Sharib Ali.

At least 19 recordsLinked to original sources

arXiv2026

LUX: A Lesion-Aware Graph-Conditioned Visual - Language Architecture for Explainable Endoscopic Captioning

The interpretation of endoscopic imagery in ulcerative colitis is complex and subjective, with variability in human assessment and subtle mucosal inflammation. Although deep learning has advanced automated analysis, most vision-language models rely on global visual embeddings that overlook the localized and relational nature of pathological evidence, limiting clinical reliability and interpretability. We introduce LUX (Lesion-aware Unified eXplainable captioning), a graph-conditioned vision-language architecture for explainable endoscopic image captioning. LUX constructs a lesion-centric scene graph from Grad-CAM and CBAM activation maps, representing pathological regions as nodes and encoding their spatial and clinical relationships. These graph embeddings are integrated into the cross-attention layers of a T5 decoder, enabling generated words to attend to specific lesion nodes rather than only to global image features. This provides direct alignment between linguistic content and pathological evidence, supporting token-level interpretability and relational reasoning. LUX outperforms strong baseline and state-of-the-art medical captioning models across BLEU, METEOR, ROUGE-L, and CIDEr, with particularly strong gains in CIDEr. It also reduces hallucinated clinical findings and improves lesion-level grounding through stronger correspondence between generated tokens and localized pathological regions.

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arXiv2026

Vis2Reg: Visibility-Aware Landmark-Free Geometric 3D--2D Registration for Liver Laparoscopy

Accurate 3D--2D liver registration, which aligns preoperative 3D models to partial, view-dependent intraoperative surface observations, is critical for AR-guided laparoscopic surgery but remains challenging due to severe occlusion, limited visibility, and the lack of 3D ground-truth supervision. Existing landmark-free approaches perform partial-to-complete geometric alignment, yet robust self-supervision under extreme partial visibility remains difficult. We propose Vis2Reg, a visibility-aware registration framework that explicitly constrains deformation using mask-consistent visible regions. We introduce a visibility-aware self-supervision that derives a visible-domain 3D supervision signal from intraoperative masks, enabled by differentiable point rasterization and mask-guided back-projection. This formulation improves robustness under severe occlusion while maintaining fully self-supervised learning. Vis2Reg combines a robust geometric rigid initialization module with an implicit neural deformation field for stable alignment. Vis2Reg achieves a Dice score of 92.6\% and a Chamfer Distance of 1.43 mm on real intraoperative datasets, with 111 ms per-frame inference time, demonstrating both accuracy and practical efficiency.

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arXiv2026

DBMF: A Dual-Branch Multimodal Framework for Out-of-Distribution Detection

The complex and dynamic real-world clinical environment demands reliable deep learning (DL) systems. Out-of-distribution (OOD) detection plays a critical role in enhancing the reliability and generalizability of DL models when encountering data that deviate from the training distribution, such as unseen disease cases. However, existing OOD detection methods typically rely either on a single visual modality or solely on image-text matching, failing to fully leverage multimodal information. To overcome the challenge, we propose a novel dual-branch multimodal framework by introducing a text-image branch and a vision branch. Our framework fully exploits multimodal representations to identify OOD samples through these two complementary branches. After training, we compute scores from the text-image branch ($S_t$) and vision branch ($S_v$), and integrate them to obtain the final OOD score $S$ that is compared with a threshold for OOD detection. Comprehensive experiments on publicly available endoscopic image datasets demonstrate that our proposed framework is robust across diverse backbones and improves state-of-the-art performance in OOD detection by up to 24.84%

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arXiv2026

A comprehensive multimodal dataset and benchmark for ulcerative colitis scoring in endoscopy

Ulcerative colitis (UC) is a chronic mucosal inflammatory condition that places patients at increased risk of colorectal cancer. Colonoscopic surveillance remains the gold standard for assessing disease activity, and reporting typically relies on standardised endoscopic scoring metrics. The most widely used is the Mayo Endoscopic Score (MES), with some centres also adopting the Ulcerative Colitis Endoscopic Index of Severity (UCEIS). Both are descriptive assessments of mucosal inflammation (MES: 0 to 3; UCEIS: 0 to 8), where higher values indicate more severe disease. However, computational methods for automatically predicting these scores remain limited, largely due to the lack of publicly available expert-annotated datasets and the absence of robust benchmarking. There is also a significant research gap in generating clinically meaningful descriptions of UC images, despite image captioning being a well-established computer vision task. Variability in endoscopic systems and procedural workflows across centres further highlights the need for multi-centre datasets to ensure algorithmic robustness and generalisability. In this work, we introduce a curated multi-centre, multi-resolution dataset that includes expert-validated MES and UCEIS labels, alongside detailed clinical descriptions. To our knowledge, this is the first comprehensive dataset that combines dual scoring metrics for classification tasks with expert-generated captions describing mucosal appearance and clinically accepted reasoning for image captioning. This resource opens new opportunities for developing clinically meaningful multimodal algorithms. In addition to the dataset, we also provide benchmarking using convolutional neural networks, vision transformers, hybrid models, and widely used multimodal vision-language captioning algorithms.

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arXiv2026

A multi-center analysis of deep learning methods for video polyp detection and segmentation

Colonic polyps are well-recognized precursors to colorectal cancer (CRC), typically detected during colonoscopy. However, the variability in appearance, location, and size of these polyps complicates their detection and removal, leading to challenges in effective surveillance, intervention, and subsequently CRC prevention. The processes of colonoscopy surveillance and polyp removal are highly reliant on the expertise of gastroenterologists and occur within the complexities of the colonic structure. As a result, there is a high rate of missed detections and incomplete removal of colonic polyps, which can adversely impact patient outcomes. Recently, automated methods that use machine learning have been developed to enhance polyps detection and segmentation, thus helping clinical processes and reducing missed rates. These advancements highlight the potential for improving diagnostic accuracy in real-time applications, which ultimately facilitates more effective patient management. Furthermore, integrating sequence data and temporal information could significantly enhance the precision of these methods by capturing the dynamic nature of polyp growth and the changes that occur over time. To rigorously investigate these challenges, data scientists and experts gastroenterologists collaborated to compile a comprehensive dataset that spans multiple centers and diverse populations. This initiative aims to underscore the critical importance of incorporating sequence data and temporal information in the development of robust automated detection and segmentation methods. This study evaluates the applicability of deep learning techniques developed in real-time clinical colonoscopy tasks using sequence data, highlighting the critical role of temporal relationships between frames in improving diagnostic precision.

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arXiv2025

RobustSurg: Tackling domain generalisation for out-of-distribution surgical scene segmentation

While recent advances in deep learning for surgical scene segmentation have demonstrated promising results on single-centre and single-imaging modality data, these methods usually do not generalise to unseen distribution (i.e., from other centres) and unseen modalities. Current literature for tackling generalisation on out-of-distribution data and domain gaps due to modality changes has been widely researched but mostly for natural scene data. However, these methods cannot be directly applied to the surgical scenes due to limited visual cues and often extremely diverse scenarios compared to the natural scene data. Inspired by these works in natural scenes to push generalisability on OOD data, we hypothesise that exploiting the style and content information in the surgical scenes could minimise the appearances, making it less variable to sudden changes such as blood or imaging artefacts. This can be achieved by performing instance normalisation and feature covariance mapping techniques for robust and generalisable feature representations. Further, to eliminate the risk of removing salient feature representation associated with the objects of interest, we introduce a restitution module within the feature learning ResNet backbone that can enable the retention of useful task-relevant features. To tackle the lack of multiclass and multicentre data for surgical scene segmentation, we also provide a newly curated dataset that can be vital for addressing generalisability in this domain. Our proposed RobustSurg obtained nearly 23% improvement on the baseline DeepLabv3+ and from 10-32% improvement on the SOTA in terms of mean IoU score on an unseen centre HeiCholSeg dataset when trained on CholecSeg8K. Similarly, RobustSurg also obtained nearly 22% improvement over the baseline and nearly 11% improvement on a recent SOTA method for the target set of the EndoUDA polyp dataset.

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arXiv2025

Surg-InvNeRF: Invertible NeRF for 3D tracking and reconstruction in surgical vision

We proposed a novel test-time optimisation (TTO) approach framed by a NeRF-based architecture for long-term 3D point tracking. Most current methods in point tracking struggle to obtain consistent motion or are limited to 2D motion. TTO approaches frame the solution for long-term tracking as optimising a function that aggregates correspondences from other specialised state-of-the-art methods. Unlike the state-of-the-art on TTO, we propose parametrising such a function with our new invertible Neural Radiance Field (InvNeRF) architecture to perform both 2D and 3D tracking in surgical scenarios. Our approach allows us to exploit the advantages of a rendering-based approach by supervising the reprojection of pixel correspondences. It adapts strategies from recent rendering-based methods to obtain a bidirectional deformable-canonical mapping, to efficiently handle a defined workspace, and to guide the rays' density. It also presents our multi-scale HexPlanes for fast inference and a new algorithm for efficient pixel sampling and convergence criteria. We present results in the STIR and SCARE datasets, for evaluating point tracking and testing the integration of kinematic data in our pipeline, respectively. In 2D point tracking, our approach surpasses the precision and accuracy of the TTO state-of-the-art methods by nearly 50% on average precision, while competing with other approaches. In 3D point tracking, this is the first TTO approach, surpassing feed-forward methods while incorporating the benefits of a deformable NeRF-based reconstruction.

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arXiv2025

NeeCo: Image Synthesis of Novel Instrument States Based on Dynamic and Deformable 3D Gaussian Reconstruction

Computer vision-based technologies significantly enhance surgical automation by advancing tool tracking, detection, and localization. However, Current data-driven approaches are data-voracious, requiring large, high-quality labeled image datasets, which limits their application in surgical data science. Our Work introduces a novel dynamic Gaussian Splatting technique to address the data scarcity in surgical image datasets. We propose a dynamic Gaussian model to represent dynamic surgical scenes, enabling the rendering of surgical instruments from unseen viewpoints and deformations with real tissue backgrounds. We utilize a dynamic training adjustment strategy to address challenges posed by poorly calibrated camera poses from real-world scenarios. Additionally, we propose a method based on dynamic Gaussians for automatically generating annotations for our synthetic data. For evaluation, we constructed a new dataset featuring seven scenes with 14,000 frames of tool and camera motion and tool jaw articulation, with a background of an ex-vivo porcine model. Using this dataset, we synthetically replicate the scene deformation from the ground truth data, allowing direct comparisons of synthetic image quality. Experimental results illustrate that our method generates photo-realistic labeled image datasets with the highest values in Peak-Signal-to-Noise Ratio (29.87). We further evaluate the performance of medical-specific neural networks trained on real and synthetic images using an unseen real-world image dataset. Our results show that the performance of models trained on synthetic images generated by the proposed method outperforms those trained with state-of-the-art standard data augmentation by 10%, leading to an overall improvement in model performances by nearly 15%.

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arXiv2025

Self-Supervised Ultrasound-Video Segmentation with Feature Prediction and 3D Localised Loss

Acquiring and annotating large datasets in ultrasound imaging is challenging due to low contrast, high noise, and susceptibility to artefacts. This process requires significant time and clinical expertise. Self-supervised learning (SSL) offers a promising solution by leveraging unlabelled data to learn useful representations, enabling improved segmentation performance when annotated data is limited. Recent state-of-the-art developments in SSL for video data include V-JEPA, a framework solely based on feature prediction, avoiding pixel level reconstruction or negative samples. We hypothesise that V-JEPA is well-suited to ultrasound imaging, as it is less sensitive to noisy pixel-level detail while effectively leveraging temporal information. To the best of our knowledge, this is the first study to adopt V-JEPA for ultrasound video data. Similar to other patch-based masking SSL techniques such as VideoMAE, V-JEPA is well-suited to ViT-based models. However, ViTs can underperform on small medical datasets due to lack of inductive biases, limited spatial locality and absence of hierarchical feature learning. To improve locality understanding, we propose a novel 3D localisation auxiliary task to improve locality in ViT representations during V-JEPA pre-training. Our results show V-JEPA with our auxiliary task improves segmentation performance significantly across various frozen encoder configurations, with gains up to 3.4\% using 100\% and up to 8.35\% using only 10\% of the training data.

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arXiv2025

A Self-Supervised Framework for Improved Generalisability in Ultrasound B-mode Image Segmentation

Ultrasound (US) imaging is clinically invaluable due to its noninvasive and safe nature. However, interpreting US images is challenging, requires significant expertise, and time, and is often prone to errors. Deep learning offers assistive solutions such as segmentation. Supervised methods rely on large, high-quality, and consistently labeled datasets, which are challenging to curate. Moreover, these methods tend to underperform on out-of-distribution data, limiting their clinical utility. Self-supervised learning (SSL) has emerged as a promising alternative, leveraging unlabeled data to enhance model performance and generalisability. We introduce a contrastive SSL approach tailored for B-mode US images, incorporating a novel Relation Contrastive Loss (RCL). RCL encourages learning of distinct features by differentiating positive and negative sample pairs through a learnable metric. Additionally, we propose spatial and frequency-based augmentation strategies for the representation learning on US images. Our approach significantly outperforms traditional supervised segmentation methods across three public breast US datasets, particularly in data-limited scenarios. Notable improvements on the Dice similarity metric include a 4% increase on 20% and 50% of the BUSI dataset, nearly 6% and 9% improvements on 20% and 50% of the BrEaST dataset, and 6.4% and 3.7% improvements on 20% and 50% of the UDIAT dataset, respectively. Furthermore, we demonstrate superior generalisability on the out-of-distribution UDIAT dataset with performance boosts of 20.6% and 13.6% compared to the supervised baseline using 20% and 50% of the BUSI and BrEaST training data, respectively. Our research highlights that domain-inspired SSL can improve US segmentation, especially under data-limited conditions.

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arXiv2025

Solving the long-tailed distribution problem by exploiting the synergies and balance of different techniques

In real-world data, long-tailed data distribution is common, making it challenging for models trained on empirical risk minimisation to learn and classify tail classes effectively. While many studies have sought to improve long tail recognition by altering the data distribution in the feature space and adjusting model decision boundaries, research on the synergy and corrective approach among various methods is limited. Our study delves into three long-tail recognition techniques: Supervised Contrastive Learning (SCL), Rare-Class Sample Generator (RSG), and Label-Distribution-Aware Margin Loss (LDAM). SCL enhances intra-class clusters based on feature similarity and promotes clear inter-class separability but tends to favour dominant classes only. When RSG is integrated into the model, we observed that the intra-class features further cluster towards the class centre, which demonstrates a synergistic effect together with SCL's principle of enhancing intra-class clustering. RSG generates new tail features and compensates for the tail feature space squeezed by SCL. Similarly, LDAM is known to introduce a larger margin specifically for tail classes; we demonstrate that LDAM further bolsters the model's performance on tail classes when combined with the more explicit decision boundaries achieved by SCL and RSG. Furthermore, SCL can compensate for the dominant class accuracy sacrificed by RSG and LDAM. Our research emphasises the synergy and balance among the three techniques, with each amplifying the strengths of the others and mitigating their shortcomings. Our experiment on long-tailed distribution datasets, using an end-to-end architecture, yields competitive results by enhancing tail class accuracy without compromising dominant class performance, achieving a balanced improvement across all classes.

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arXiv2024

NCDD: Nearest Centroid Distance Deficit for Out-Of-Distribution Detection in Gastrointestinal Vision

The integration of deep learning tools in gastrointestinal vision holds the potential for significant advancements in diagnosis, treatment, and overall patient care. A major challenge, however, is these tools' tendency to make overconfident predictions, even when encountering unseen or newly emerging disease patterns, undermining their reliability. We address this critical issue of reliability by framing it as an out-of-distribution (OOD) detection problem, where previously unseen and emerging diseases are identified as OOD examples. However, gastrointestinal images pose a unique challenge due to the overlapping feature representations between in- Distribution (ID) and OOD examples. Existing approaches often overlook this characteristic, as they are primarily developed for natural image datasets, where feature distinctions are more apparent. Despite the overlap, we hypothesize that the features of an in-distribution example will cluster closer to the centroids of their ground truth class, resulting in a shorter distance to the nearest centroid. In contrast, OOD examples maintain an equal distance from all class centroids. Based on this observation, we propose a novel nearest-centroid distance deficit (NCCD) score in the feature space for gastrointestinal OOD detection. Evaluations across multiple deep learning architectures and two publicly available benchmarks, Kvasir2 and Gastrovision, demonstrate the effectiveness of our approach compared to several state-of-the-art methods. The code and implementation details are publicly available at: https://github.com/bhattarailab/NCDD

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arXiv2024

Self-supervised Monocular Depth and Pose Estimation for Endoscopy with Latent Priors

Accurate 3D mapping in endoscopy enables quantitative, holistic lesion characterization within the gastrointestinal (GI) tract, requiring reliable depth and pose estimation. However, endoscopy systems are monocular, and existing methods relying on synthetic datasets or complex models often lack generalizability in challenging endoscopic conditions. We propose a robust self-supervised monocular depth and pose estimation framework that incorporates a Generative Latent Bank and a Variational Autoencoder (VAE). The Generative Latent Bank leverages extensive depth scenes from natural images to condition the depth network, enhancing realism and robustness of depth predictions through latent feature priors. For pose estimation, we reformulate it within a VAE framework, treating pose transitions as latent variables to regularize scale, stabilize z-axis prominence, and improve x-y sensitivity. This dual refinement pipeline enables accurate depth and pose predictions, effectively addressing the GI tract's complex textures and lighting. Extensive evaluations on SimCol and EndoSLAM datasets confirm our framework's superior performance over published self-supervised methods in endoscopic depth and pose estimation.

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arXiv2024

Tackling domain generalization for out-of-distribution endoscopic imaging

While recent advances in deep learning (DL) for surgical scene segmentation have yielded promising results on single-center and single-imaging modality data, these methods usually do not generalize well to unseen distributions or modalities. Even though human experts can identify visual appearances, DL methods often fail to do so when data samples do not follow a similar distribution. Current literature addressing domain gaps in modality changes has focused primarily on natural scene data. However, these methods cannot be directly applied to endoscopic data, as visual cues in such data are more limited compared to natural scenes. In this work, we exploit both style and content information in images by performing instance normalization and feature covariance mapping techniques to preserve robust and generalizable feature representations. Additionally, to avoid the risk of removing salient feature representations associated with objects of interest, we introduce a restitution module within the feature-learning ResNet backbone that retains useful task-relevant features. Our proposed method shows a 13.7% improvement over the baseline DeepLabv3+ and nearly an 8% improvement over recent state-of-the-art (SOTA) methods for the target (different modality) set of the EndoUDA polyp dataset. Similarly, our method achieved a 19% improvement over the baseline and 6% over the best-performing SOTA method on the EndoUDA Barrett's esophagus (BE) dataset.

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arXiv2024

Domain Generalization for Endoscopic Image Segmentation by Disentangling Style-Content Information and SuperPixel Consistency

Frequent monitoring is necessary to stratify individuals based on their likelihood of developing gastrointestinal (GI) cancer precursors. In clinical practice, white-light imaging (WLI) and complementary modalities such as narrow-band imaging (NBI) and fluorescence imaging are used to assess risk areas. However, conventional deep learning (DL) models show degraded performance due to the domain gap when a model is trained on one modality and tested on a different one. In our earlier approach, we used a superpixel-based method referred to as "SUPRA" to effectively learn domain-invariant information using color and space distances to generate groups of pixels. One of the main limitations of this earlier work is that the aggregation does not exploit structural information, making it suboptimal for segmentation tasks, especially for polyps and heterogeneous color distributions. Therefore, in this work, we propose an approach for style-content disentanglement using instance normalization and instance selective whitening (ISW) for improved domain generalization when combined with SUPRA. We evaluate our approach on two datasets: EndoUDA Barrett's Esophagus and EndoUDA polyps, and compare its performance with three state-of-the-art (SOTA) methods. Our findings demonstrate a notable enhancement in performance compared to both baseline and SOTA methods across the target domain data. Specifically, our approach exhibited improvements of 14%, 10%, 8%, and 18% over the baseline and three SOTA methods on the polyp dataset. Additionally, it surpassed the second-best method (EndoUDA) on the Barrett's Esophagus dataset by nearly 2%.

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arXiv2024

SSTFB: Leveraging self-supervised pretext learning and temporal self-attention with feature branching for real-time video polyp segmentation

Polyps are early cancer indicators, so assessing occurrences of polyps and their removal is critical. They are observed through a colonoscopy screening procedure that generates a stream of video frames. Segmenting polyps in their natural video screening procedure has several challenges, such as the co-existence of imaging artefacts, motion blur, and floating debris. Most existing polyp segmentation algorithms are developed on curated still image datasets that do not represent real-world colonoscopy. Their performance often degrades on video data. We propose a video polyp segmentation method that performs self-supervised learning as an auxiliary task and a spatial-temporal self-attention mechanism for improved representation learning. Our end-to-end configuration and joint optimisation of losses enable the network to learn more discriminative contextual features in videos. Our experimental results demonstrate an improvement with respect to several state-of-the-art (SOTA) methods. Our ablation study also confirms that the choice of the proposed joint end-to-end training improves network accuracy by over 3% and nearly 10% on both the Dice similarity coefficient and intersection-over-union compared to the recently proposed method PNS+ and Polyp-PVT, respectively. Results on previously unseen video data indicate that the proposed method generalises.

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arXiv2024

An objective comparison of methods for augmented reality in laparoscopic liver resection by preoperative-to-intraoperative image fusion

Augmented reality for laparoscopic liver resection is a visualisation mode that allows a surgeon to localise tumours and vessels embedded within the liver by projecting them on top of a laparoscopic image. Preoperative 3D models extracted from CT or MRI data are registered to the intraoperative laparoscopic images during this process. In terms of 3D-2D fusion, most of the algorithms make use of anatomical landmarks to guide registration. These landmarks include the liver's inferior ridge, the falciform ligament, and the occluding contours. They are usually marked by hand in both the laparoscopic image and the 3D model, which is time-consuming and may contain errors if done by a non-experienced user. Therefore, there is a need to automate this process so that augmented reality can be used effectively in the operating room. We present the Preoperative-to-Intraoperative Laparoscopic Fusion Challenge (P2ILF), held during the Medical Imaging and Computer Assisted Interventions (MICCAI 2022) conference, which investigates the possibilities of detecting these landmarks automatically and using them in registration. The challenge was divided into two tasks: 1) A 2D and 3D landmark detection task and 2) a 3D-2D registration task. The teams were provided with training data consisting of 167 laparoscopic images and 9 preoperative 3D models from 9 patients, with the corresponding 2D and 3D landmark annotations. A total of 6 teams from 4 countries participated, whose proposed methods were evaluated on 16 images and two preoperative 3D models from two patients. All the teams proposed deep learning-based methods for the 2D and 3D landmark segmentation tasks and differentiable rendering-based methods for the registration task. Based on the experimental outcomes, we propose three key hypotheses that determine current limitations and future directions for research in this domain.

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arXiv2023

Multi-task learning with cross-task consistency for improved depth estimation in colonoscopy

Colonoscopy screening is the gold standard procedure for assessing abnormalities in the colon and rectum, such as ulcers and cancerous polyps. Measuring the abnormal mucosal area and its 3D reconstruction can help quantify the surveyed area and objectively evaluate disease burden. However, due to the complex topology of these organs and variable physical conditions, for example, lighting, large homogeneous texture, and image modality estimating distance from the camera aka depth) is highly challenging. Moreover, most colonoscopic video acquisition is monocular, making the depth estimation a non-trivial problem. While methods in computer vision for depth estimation have been proposed and advanced on natural scene datasets, the efficacy of these techniques has not been widely quantified on colonoscopy datasets. As the colonic mucosa has several low-texture regions that are not well pronounced, learning representations from an auxiliary task can improve salient feature extraction, allowing estimation of accurate camera depths. In this work, we propose to develop a novel multi-task learning (MTL) approach with a shared encoder and two decoders, namely a surface normal decoder and a depth estimator decoder. Our depth estimator incorporates attention mechanisms to enhance global context awareness. We leverage the surface normal prediction to improve geometric feature extraction. Also, we apply a cross-task consistency loss among the two geometrically related tasks, surface normal and camera depth. We demonstrate an improvement of 14.17% on relative error and 10.4% improvement on $\delta_{1}$ accuracy over the most accurate baseline state-of-the-art BTS approach. All experiments are conducted on a recently released C3VD dataset; thus, we provide a first benchmark of state-of-the-art methods.

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