3D Reconstruction of the Human Colon from Capsule Endoscope Video

As the number of people affected by diseases in the gastrointestinal system is ever-increasing, a higher demand on preventive screening is inevitable. This will significantly increase the workload on gastroenterologists. To help reduce the workload, tools from computer vision may be helpful. In this paper, we investigate the possibility of constructing 3D models of whole sections of the human colon using image sequences from wireless capsule endoscope video, providing enhanced viewing for gastroenterologists. As capsule endoscope images contain distortion and artifacts non-ideal for many 3D reconstruction algorithms, the problem is challenging. However, recent developments of virtual graphics-based models of the human gastrointestinal system, where distortion and artifacts can be enabled or disabled, makes it possible to ``dissect'' the problem. The graphical model also provides a ground truth, enabling computation of geometric distortion introduced by the 3D reconstruction method. In this paper, most distortions and artifacts are left out to determine if it is feasible to reconstruct whole sections of the human gastrointestinal system by existing methods. We demonstrate that 3D reconstruction is possible using simultaneous localization and mapping. Further, to reconstruct the gastrointestinal wall surface from resulting point clouds, varying greatly in density, Poisson surface reconstruction is a good option. The results are promising, encouraging further research on this problem.

Terrain-Informed Self-Supervised Learning: Enhancing Building Footprint Extraction from LiDAR Data with Limited Annotations

Estimating building footprint maps from geospatial data is of paramount importance in urban planning, development, disaster management, and various other applications. Deep learning methodologies have gained prominence in building segmentation maps, offering the promise of precise footprint extraction without extensive post-processing. However, these methods face challenges in generalization and label efficiency, particularly in remote sensing, where obtaining accurate labels can be both expensive and time-consuming. To address these challenges, we propose terrain-aware self-supervised learning, tailored to remote sensing, using digital elevation models from LiDAR data. We propose to learn a model to differentiate between bare Earth and superimposed structures enabling the network to implicitly learn domain-relevant features without the need for extensive pixel-level annotations. We test the effectiveness of our approach by evaluating building segmentation performance on test datasets with varying label fractions. Remarkably, with only 1% of the labels (equivalent to 25 labeled examples), our method improves over ImageNet pre-training, showing the advantage of leveraging unlabeled data for feature extraction in the domain of remote sensing. The performance improvement is more pronounced in few-shot scenarios and gradually closes the gap with ImageNet pre-training as the label fraction increases. We test on a dataset characterized by substantial distribution shifts and labeling errors to demonstrate the generalizability of our approach. When compared to other baselines, including ImageNet pretraining and more complex architectures, our approach consistently performs better, demonstrating the efficiency and effectiveness of self-supervised terrain-aware feature learning.

Learning Pairwise Interaction for Generalizable DeepFake Detection

A fast-paced development of DeepFake generation techniques challenge the detection schemes designed for known type DeepFakes. A reliable Deepfake detection approach must be agnostic to generation types, which can present diverse quality and appearance. Limited generalizability across different generation schemes will restrict the wide-scale deployment of detectors if they fail to handle unseen attacks in an open set scenario. We propose a new approach, Multi-Channel Xception Attention Pairwise Interaction (MCX-API), that exploits the power of pairwise learning and complementary information from different color space representations in a fine-grained manner. We first validate our idea on a publicly available dataset in a intra-class setting (closed set) with four different Deepfake schemes. Further, we report all the results using balanced-open-set-classification (BOSC) accuracy in an inter-class setting (open-set) using three public datasets. Our experiments indicate that our proposed method can generalize better than the state-of-the-art Deepfakes detectors. We obtain 98.48% BOSC accuracy on the FF++ dataset and 90.87% BOSC accuracy on the CelebDF dataset suggesting a promising direction for generalization of DeepFake detection. We further utilize t-SNE and attention maps to interpret and visualize the decision-making process of our proposed network. https://github.com/xuyingzhongguo/MCX-API

Evaluating clinical diversity and plausibility of synthetic capsule endoscopic images

Wireless Capsule Endoscopy (WCE) is being increasingly used as an alternative imaging modality for complete and non-invasive screening of the gastrointestinal tract. Although this is advantageous in reducing unnecessary hospital admissions, it also demands that a WCE diagnostic protocol be in place so larger populations can be effectively screened. This calls for training and education protocols attuned specifically to this modality. Like training in other modalities such as traditional endoscopy, CT, MRI, etc., a WCE training protocol would require an atlas comprising of a large corpora of images that show vivid descriptions of pathologies and abnormalities, ideally observed over a period of time. Since such comprehensive atlases are presently lacking in WCE, in this work, we propose a deep learning method for utilizing already available studies across different institutions for the creation of a realistic WCE atlas using StyleGAN. We identify clinically relevant attributes in WCE such that synthetic images can be generated with selected attributes on cue. Beyond this, we also simulate several disease progression scenarios. The generated images are evaluated for realism and plausibility through three subjective online experiments with the participation of eight gastroenterology experts from three geographical locations and a variety of years of experience. The results from the experiments indicate that the images are highly realistic and the disease scenarios plausible. The images comprising the atlas are available publicly for use in training applications as well as supplementing real datasets for deep learning.

This changes to that : Combining causal and non-causal explanations to generate disease progression in capsule endoscopy

Due to the unequivocal need for understanding the decision processes of deep learning networks, both modal-dependent and model-agnostic techniques have become very popular. Although both of these ideas provide transparency for automated decision making, most methodologies focus on either using the modal-gradients (model-dependent) or ignoring the model internal states and reasoning with a model's behavior/outcome (model-agnostic) to instances. In this work, we propose a unified explanation approach that given an instance combines both model-dependent and agnostic explanations to produce an explanation set. The generated explanations are not only consistent in the neighborhood of a sample but can highlight causal relationships between image content and the outcome. We use Wireless Capsule Endoscopy (WCE) domain to illustrate the effectiveness of our explanations. The saliency maps generated by our approach are comparable or better on the softmax information score.

A Comprehensive Analysis of AI Biases in DeepFake Detection With Massively Annotated Databases

In recent years, image and video manipulations with DeepFake have become a severe concern for security and society. Therefore, many detection models and databases have been proposed to detect DeepFake data reliably. However, there is an increased concern that these models and training databases might be biased and thus, cause DeepFake detectors to fail. In this work, we tackle these issues by (a) providing large-scale demographic and non-demographic attribute annotations of 41 different attributes for five popular DeepFake datasets and (b) comprehensively analysing AI-bias of multiple state-of-the-art DeepFake detection models on these databases. The investigation analyses the influence of a large variety of distinctive attributes (from over 65M labels) on the detection performance, including demographic (age, gender, ethnicity) and non-demographic (hair, skin, accessories, etc.) information. The results indicate that investigated databases lack diversity and, more importantly, show that the utilised DeepFake detection models are strongly biased towards many investigated attributes. Moreover, the results show that the models' decision-making might be based on several questionable (biased) assumptions, such if a person is smiling or wearing a hat. Depending on the application of such DeepFake detection methods, these biases can lead to generalizability, fairness, and security issues. We hope that the findings of this study and the annotation databases will help to evaluate and mitigate bias in future DeepFake detection techniques. Our annotation datasets are made publicly available.

From Labels to Priors in Capsule Endoscopy: A Prior Guided Approach for Improving Generalization with Few Labels

The lack of generalizability of deep learning approaches for the automated diagnosis of pathologies in Wireless Capsule Endoscopy (WCE) has prevented any significant advantages from trickling down to real clinical practices. As a result, disease management using WCE continues to depend on exhaustive manual investigations by medical experts. This explains its limited use despite several advantages. Prior works have considered using higher quality and quantity of labels as a way of tackling the lack of generalization, however this is hardly scalable considering pathology diversity not to mention that labeling large datasets encumbers the medical staff additionally. We propose using freely available domain knowledge as priors to learn more robust and generalizable representations. We experimentally show that domain priors can benefit representations by acting in proxy of labels, thereby significantly reducing the labeling requirement while still enabling fully unsupervised yet pathology-aware learning. We use the contrastive objective along with prior-guided views during pretraining, where the view choices inspire sensitivity to pathological information. Extensive experiments on three datasets show that our method performs better than (or closes gap with) the state-of-the-art in the domain, establishing a new benchmark in pathology classification and cross-dataset generalization, as well as scaling to unseen pathology categories.

Learning More for Free - A Multi Task Learning Approach for Improved Pathology Classification in Capsule Endoscopy

The progress in Computer Aided Diagnosis (CADx) of Wireless Capsule Endoscopy (WCE) is thwarted by the lack of data. The inadequacy in richly representative healthy and abnormal conditions results in isolated analyses of pathologies, that can not handle realistic multi-pathology scenarios. In this work, we explore how to learn more for free, from limited data through solving a WCE multicentric, multi-pathology classification problem. Learning more implies to learning more than full supervision would allow with the same data. This is done by combining self supervision with full supervision, under multi task learning. Additionally, we draw inspiration from the Human Visual System (HVS) in designing self supervision tasks and investigate if seemingly ineffectual signals within the data itself can be exploited to gain performance, if so, which signals would be better than others. Further, we present our analysis of the high level features as a stepping stone towards more robust multi-pathology CADx in WCE.

Advanced Image Enhancement Method for Distant Vessels and Structures in Capsule Endoscopy

This paper proposes an advanced method for contrast enhancement of capsule endoscopic images, with the main objective to obtain sufficient information about the vessels and structures in more distant (or darker) parts of capsule endoscopic images. The proposed method (PM) combines two algorithms for the enhancement of darker and brighter areas of capsule endoscopic images, respectively. The half-unit weighted bilinear algorithm (HWB) proposed in our previous work is used to enhance darker areas according to the darker map content of its HSV's component V. Enhancement of brighter areas is achieved thanks to the novel thresholded weighted-bilinear algorithm (TWB) developed to avoid overexposure and enlargement of specular highlight spots while preserving the hue, in such areas. The TWB performs enhancement operations following a gradual increment of the brightness of the brighter map content of its HSV's component V. In other words, the TWB decreases its averaged-weights as the intensity content of the component V increases. Extensive experimental demonstrations were conducted, and based on evaluation of the reference and PM enhanced images, a gastroenterologist ({\O}H) concluded that the PM enhanced images were the best ones based on the information about the vessels, contrast in the images, and the view or visibility of the structures in more distant parts of the capsule endoscopy images.

2018 Robotic Scene Segmentation Challenge

In 2015 we began a sub-challenge at the EndoVis workshop at MICCAI in Munich using endoscope images of ex-vivo tissue with automatically generated annotations from robot forward kinematics and instrument CAD models. However, the limited background variation and simple motion rendered the dataset uninformative in learning about which techniques would be suitable for segmentation in real surgery. In 2017, at the same workshop in Quebec we introduced the robotic instrument segmentation dataset with 10 teams participating in the challenge to perform binary, articulating parts and type segmentation of da Vinci instruments. This challenge included realistic instrument motion and more complex porcine tissue as background and was widely addressed with modifications on U-Nets and other popular CNN architectures. In 2018 we added to the complexity by introducing a set of anatomical objects and medical devices to the segmented classes. To avoid over-complicating the challenge, we continued with porcine data which is dramatically simpler than human tissue due to the lack of fatty tissue occluding many organs.