Transforming spatio-temporal self-attention using action embedding for skeleton-based action recognition

Over the past few years, skeleton-based action recognition has attracted great success because the skeleton data is immune to illumination variation, view-point variation, background clutter, scaling, and camera motion. However, effective modeling of the latent information of skeleton data is still a challenging problem. Therefore, in this paper, we propose a novel idea of action embedding with a self-attention Transformer network for skeleton-based action recognition. Our proposed technology mainly comprises of two modules as, i) action embedding and ii) self-attention Transformer. The action embedding encodes the relationship between corresponding body joints (e.g., joints of both hands move together for performing clapping action) and thus captures the spatial features of joints. Meanwhile, temporal features and dependencies of body joints are modeled using Transformer architecture. Our method works in a single-stream (end-to-end) fashion, where MLP is used for classification. We carry out an ablation study and evaluate the performance of our model on a small-scale SYSU-3D dataset and large-scale NTU-RGB+D and NTU-RGB+D 120 datasets where the results establish that our method performs better than other state-of-the-art architectures.publishedVersio

Balancing Privacy and Progress in Artificial Intelligence: Anonymization in Histopathology for Biomedical Research and Education

The advancement of biomedical research heavily relies on access to large amounts of medical data. In the case of histopathology, Whole Slide Images (WSI) and clinicopathological information are valuable for developing Artificial Intelligence (AI) algorithms for Digital Pathology (DP). Transferring medical data "as open as possible" enhances the usability of the data for secondary purposes but poses a risk to patient privacy. At the same time, existing regulations push towards keeping medical data "as closed as necessary" to avoid re-identification risks. Generally, these legal regulations require the removal of sensitive data but do not consider the possibility of data linkage attacks due to modern image-matching algorithms. In addition, the lack of standardization in DP makes it harder to establish a single solution for all formats of WSIs. These challenges raise problems for bio-informatics researchers in balancing privacy and progress while developing AI algorithms. This paper explores the legal regulations and terminologies for medical data-sharing. We review existing approaches and highlight challenges from the histopathological perspective. We also present a data-sharing guideline for histological data to foster multidisciplinary research and education.Comment: Accepted to FAIEMA 202

Enhancing Prostate Cancer Diagnosis with Deep Learning: A Study using mpMRI Segmentation and Classification

Prostate cancer (PCa) is a severe disease among men globally. It is important to identify PCa early and make a precise diagnosis for effective treatment. For PCa diagnosis, Multi-parametric magnetic resonance imaging (mpMRI) emerged as an invaluable imaging modality that offers a precise anatomical view of the prostate gland and its tissue structure. Deep learning (DL) models can enhance existing clinical systems and improve patient care by locating regions of interest for physicians. Recently, DL techniques have been employed to develop a pipeline for segmenting and classifying different cancer types. These studies show that DL can be used to increase diagnostic precision and give objective results without variability. This work uses well-known DL models for the classification and segmentation of mpMRI images to detect PCa. Our implementation involves four pipelines; Semantic DeepSegNet with ResNet50, DeepSegNet with recurrent neural network (RNN), U-Net with RNN, and U-Net with a long short-term memory (LSTM). Each segmentation model is paired with a different classifier to evaluate the performance using different metrics. The results of our experiments show that the pipeline that uses the combination of U-Net and the LSTM model outperforms all other combinations, excelling in both segmentation and classification tasks.Comment: Accepted at CISCON-202

The Devil is in the Details: Whole Slide Image Acquisition and Processing for Artifacts Detection, Color Variation, and Data Augmentation: A Review

Whole Slide Images (WSI) are widely used in histopathology for research and the diagnosis of different types of cancer. The preparation and digitization of histological tissues leads to the introduction of artifacts and variations that need to be addressed before the tissues are analyzed. WSI preprocessing can significantly improve the performance of computational pathology systems and is often used to facilitate human or machine analysis. Color preprocessing techniques are frequently mentioned in the literature, while other areas are usually ignored. In this paper, we present a detailed study of the state-of-the-art in three different areas of WSI preprocessing: Artifacts detection, color variation, and the emerging field of pathology-specific data augmentation. We include a summary of evaluation techniques along with a discussion of possible limitations and future research directions for new methods.European Commission 860627Ministerio de Ciencia e Innovacion (MCIN)/Agencia Estatal de Investigacion (AEI) PID2019-105142RB-C22Fondo Europeo de Desarrollo Regional (FEDER)/Junta de Andalucia-Consejeria de Transformacion Economica, Industria, Conocimiento y Universidades B-TIC-324-UGR20Instituto de Salud Carlos III Spanish Government European Commission BES-2017-08158

Vision Transformers for Small Histological Datasets Learned through Knowledge Distillation

Computational Pathology (CPATH) systems have the potential to automate diagnostic tasks. However, the artifacts on the digitized histological glass slides, known as Whole Slide Images (WSIs), may hamper the overall performance of CPATH systems. Deep Learning (DL) models such as Vision Transformers (ViTs) may detect and exclude artifacts before running the diagnostic algorithm. A simple way to develop robust and generalized ViTs is to train them on massive datasets. Unfortunately, acquiring large medical datasets is expensive and inconvenient, prompting the need for a generalized artifact detection method for WSIs. In this paper, we present a student-teacher recipe to improve the classification performance of ViT for the air bubbles detection task. ViT, trained under the student-teacher framework, boosts its performance by distilling existing knowledge from the high-capacity teacher model. Our best-performing ViT yields 0.961 and 0.911 F1-score and MCC, respectively, observing a 7% gain in MCC against stand-alone training. The proposed method presents a new perspective of leveraging knowledge distillation over transfer learning to encourage the use of customized transformers for efficient preprocessing pipelines in the CPATH systems.Comment: Accepted at PAKDD 202

Towards Privacy-, Budget-, and Deadline-Aware Service Optimization for Large Medical Image Processing across Hybrid Clouds

Efficiently processing medical images, such as whole slide images in digital pathology, is essential for timely diagnosing high-risk diseases. However, this demands advanced computing infrastructure, e.g., GPU servers for deep learning inferencing, and local processing is time-consuming and costly. Besides, privacy concerns further complicate the employment of remote cloud infrastructures. While previous research has explored privacy and security-aware workflow scheduling in hybrid clouds for distributed processing, privacy-preserving data splitting, optimizing the service allocation of outsourcing computation on split data to the cloud, and privacy evaluation for large medical images still need to be addressed. This study focuses on tailoring a virtual infrastructure within a hybrid cloud environment and scheduling the image processing services while preserving privacy. We aim to minimize the use of untrusted nodes, lower monetary costs, and reduce execution time under privacy, budget, and deadline requirements. We consider a two-phase solution and develop 1) a privacy-preserving data splitting algorithm and 2) a greedy Pareto front-based algorithm for optimizing the service allocation. We conducted experiments with real and simulated data to validate and compare our method with a baseline. The results show that our privacy mechanism design outperforms the baseline regarding the average lower band on individual privacy and information gain for privacy evaluation. In addition, our approach can obtain various Pareto optimal-based allocations with users' preferences on the maximum number of untrusted nodes, budget, and time threshold. Our solutions often dominate the baseline's solution and are superior on a tight budget. Specifically, our approach has been ahead of baseline, up to 85.2% and 6.8% in terms of the total financial and time costs, respectively

Are you sure it's an artifact?:Artifact detection and uncertainty quantification in histological images

Modern cancer diagnostics involves extracting tissue specimens from suspicious areas and conducting histotechnical procedures to prepare a digitized glass slide, called Whole Slide Image (WSI), for further examination. These procedures frequently introduce different types of artifacts in the obtained WSI, and histological artifacts might influence Computational Pathology (CPATH) systems further down to a diagnostic pipeline if not excluded or handled. Deep Convolutional Neural Networks (DCNNs) have achieved promising results for the detection of some WSI artifacts, however, they do not incorporate uncertainty in their predictions. This paper proposes an uncertainty-aware Deep Kernel Learning (DKL) model to detect blurry areas and folded tissues, two types of artifacts that can appear in WSIs. The proposed probabilistic model combines a CNN feature extractor and a sparse Gaussian Processes (GPs) classifier, which improves the performance of current state-of-the-art artifact detection DCNNs and provides uncertainty estimates. We achieved 0.996 and 0.938 F1 scores for blur and folded tissue detection on unseen data, respectively. In extensive experiments, we validated the DKL model on unseen data from external independent cohorts with different staining and tissue types, where it outperformed DCNNs. Interestingly, the DKL model is more confident in the correct predictions and less in the wrong ones. The proposed DKL model can be integrated into the preprocessing pipeline of CPATH systems to provide reliable predictions and possibly serve as a quality control tool.</p

Are you sure it's an artifact?:Artifact detection and uncertainty quantification in histological images

Modern cancer diagnostics involves extracting tissue specimens from suspicious areas and conducting histotechnical procedures to prepare a digitized glass slide, called Whole Slide Image (WSI), for further examination. These procedures frequently introduce different types of artifacts in the obtained WSI, and histological artifacts might influence Computational Pathology (CPATH) systems further down to a diagnostic pipeline if not excluded or handled. Deep Convolutional Neural Networks (DCNNs) have achieved promising results for the detection of some WSI artifacts, however, they do not incorporate uncertainty in their predictions. This paper proposes an uncertainty-aware Deep Kernel Learning (DKL) model to detect blurry areas and folded tissues, two types of artifacts that can appear in WSIs. The proposed probabilistic model combines a CNN feature extractor and a sparse Gaussian Processes (GPs) classifier, which improves the performance of current state-of-the-art artifact detection DCNNs and provides uncertainty estimates. We achieved 0.996 and 0.938 F1 scores for blur and folded tissue detection on unseen data, respectively. In extensive experiments, we validated the DKL model on unseen data from external independent cohorts with different staining and tissue types, where it outperformed DCNNs. Interestingly, the DKL model is more confident in the correct predictions and less in the wrong ones. The proposed DKL model can be integrated into the preprocessing pipeline of CPATH systems to provide reliable predictions and possibly serve as a quality control tool.</p

Quantifying the effect of color processing on blood and damaged tissue detection in Whole Slide Images

Histological tissue examination has been a longstanding practice for cancer diagnosis where pathologists identify the presence of tumors on glass slides. Slides acquired from laboratory routine may contain unintentional artifacts due to complications in surgical resection. Blood and damaged tissue artifacts are two common problems associated with transurethral resection of the bladder tumor. Differences in histotechnical procedures among laboratories may also result in color variations and minor inconsistencies in outcome. A digitized version of a glass slide known as a whole slide image (WSI) holds enormous potential for automated diagnostics. The presence of irrelevant areas in a WSI undermines diagnostic value for pathologists as well as computational pathology (CPATH) systems. Therefore, automatic detection and exclusion of diagnostically irrelevant areas may lead to more reliable predictions. In this paper, we are detecting blood and damaged tissue against diagnostically relevant tissue. We gauge the effectiveness of transfer learning against training from scratch. Best models give 0.99 and 0.89 F1 scores for blood and damaged tissue detection. Since blood and damaged tissue have subtle color differences, we assess the impact of color processing methods on the binary classification performance of five well-known architectures. Finally, we remove the color to understand its importance against morphology on classification performance.acceptedVersio

Invasive cancerous area detection in non-muscle invasive bladder cancer whole slide images

Bladder cancer patients’ stratification into risk groups relies on grade, stage and clinical factors. For non-muscle invasive bladder cancer, T1 tumours that invade the subepithelial tissue are high-risk lesions with a high probability to progress into an aggressive muscle-invasive disease. Detecting invasive cancerous areas is the main factor for dictating the treatment strategy for the patient. However, defining invasion is often subject to intra/interobserver variability among pathologists, thus leading to over or undertreatment. Computer-aided diagnosis systems can help pathologists reduce overheads and erratic reproducibility. We propose a multi-scale model that detects invasive cancerous areas patterns across the whole slide image. The model extracts tiles of different tissue types at multiple magnification levels and processes them to predict invasive patterns based on local and regional information for accurate T1 staging. Our proposed method yields an F1 score of 71.9, in controlled settings 74.9, and without infiltration 90.0.acceptedVersio