Multiplex Cellular Communities in Multi-Gigapixel Colorectal Cancer Histology Images for Tissue Phenotyping

Neural Graph Refinement for Robust Recognition of Nuclei Communities in Histopathological Landscape

Accurate classification of nuclei communities is an important step towards timely treating the cancer spread. Graph theory provides an elegant way to represent and analyze nuclei communities within the histopathological landscape in order to perform tissue phenotyping and tumor profiling tasks. Many researchers have worked on recognizing nuclei regions within the histology images in order to grade cancerous progression. However, due to the high structural similarities between nuclei communities, defining a model that can accurately differentiate between nuclei pathological patterns still needs to be solved. To surmount this challenge, we present a novel approach, dubbed neural graph refinement, that enhances the capabilities of existing models to perform nuclei recognition tasks by employing graph representational learning and broadcasting processes. Based on the physical interaction of the nuclei, we first construct a fully connected graph in which nodes represent nuclei and adjacent nodes are connected to each other via an undirected edge. For each edge and node pair, appearance and geometric features are computed and are then utilized for generating the neural graph embeddings. These embeddings are used for diffusing contextual information to the neighboring nodes, all along a path traversing the whole graph to infer global information over an entire nuclei network and predict pathologically meaningful communities. Through rigorous evaluation of the proposed scheme across four public datasets, we showcase that learning such communities through neural graph refinement produces better results that outperform state-of-the-art methods.

Interpretable Inference and Classification of Tissue Types in Histological Colorectal Cancer Slides Based on Ensembles Adaptive Boosting Prototype Tree

Digital pathology images are treated as the "gold standard" for the diagnosis of colorectal lesions, especially colon cancer. Real-time, objective and accurate inspection results will assist clinicians to choose symptomatic treatment in a timely manner, which is of great significance in clinical medicine. However, Manual methods suffers from long inspection cycle and serious reliance on subjective interpretation. It is also a challenging task for existing computer-aided diagnosis methods to obtain models that are both accurate and interpretable. Models that exhibit high accuracy are always more complex and opaque, while interpretable models may lack the necessary accuracy. Therefore, the framework of ensemble adaptive boosting prototype tree is proposed to predict the colorectal pathology images and provide interpretable inference by visualizing the decision-making process in each base learner. The results showed that the proposed method could effectively address the "accuracy-interpretability trade-off" issue by ensemble of m adaptive boosting neural prototype trees. The superior performance of the framework provides a novel paradigm for interpretable inference and high-precision prediction of pathology image patches in computational pathology.

Lung cancer lesion detection in histopathology images using graph-based sparse PCA network

Early detection of lung cancer is critical for improvement of patient survival. To address the clinical need for efficacious treatments, genetically engineered mouse models (GEMM) have become integral in identifying and evaluating the molecular underpinnings of this complex disease that may be exploited as therapeutic targets. Assessment of GEMM tumor burden on histopathological sections performed by manual inspection is both time consuming and prone to subjective bias. Therefore, an interplay of needs and challenges exists for computer-aided diagnostic tools, for accurate and efficient analysis of these histopathology images. In this paper, we propose a simple machine learning approach called the graph-based sparse principal component analysis (GS-PCA) network, for automated detection of cancerous lesions on histological lung slides stained by hematoxylin and eosin (H&E). Our method comprises four steps: 1) cascaded graph-based sparse PCA, 2) PCA binary hashing, 3) block-wise histograms, and 4) support vector machine (SVM) classification. In our proposed architecture, graph-based sparse PCA is employed to learn the filter banks of the multiple stages of a convolutional network. This is followed by PCA hashing and block histograms for indexing and pooling. The meaningful features extracted from this GS-PCA are then fed to an SVM classifier. We evaluate the performance of the proposed algorithm on H&E slides obtained from an inducible K-ras^G12D lung cancer mouse model using precision/recall rates, F_β-score, Tanimoto coefficient, and area under the curve (AUC) of the receiver operator characteristic (ROC) and show that our algorithm is efficient and provides improved detection accuracy compared to existing algorithms.

JE, Tudzarovski N, Meinke K, Sugars RV. A graph neural network framework for mapping histological topology in oral mucosal tissue

BACKGROUND

Histological feature representation is advantageous for computer aided diagnosis (CAD) and disease classification when using predictive techniques based on machine learning. Explicit feature representations in computer tissue models can assist explainability of machine learning predictions. Different approaches to feature representation within digital tissue images have been proposed. Cell-graphs have been demonstrated to provide precise and general constructs that can model both low- and high-level features. The basement membrane is high-level tissue architecture, and interactions across the basement membrane are involved in multiple disease processes. Thus, the basement membrane is an important histological feature to study from a cell-graph and machine learning perspective.

RESULTS

We present a two stage machine learning pipeline for generating a cell-graph from a digital H &E stained tissue image. Using a combination of convolutional neural networks for visual analysis and graph neural networks exploiting node and edge labels for topological analysis, the pipeline is shown to predict both low- and high-level histological features in oral mucosal tissue with good accuracy.

CONCLUSIONS

Convolutional and graph neural networks are complementary technologies for learning, representing and predicting local and global histological features employing node and edge labels. Their combination is potentially widely applicable in histopathology image analysis and can enhance explainability in CAD tools for disease prediction.

Hierarchical Spatiotemporal Graph Regularized Discriminative Correlation Filter for Visual Object Tracking

Visual object tracking is a fundamental and challenging task in many high-level vision and robotics applications. It is typically formulated by estimating the target appearance model between consecutive frames. Discriminative correlation filters (DCFs) and their variants have achieved promising speed and accuracy for visual tracking in many challenging scenarios. However, because of the unwanted boundary effects and lack of geometric constraints, these methods suffer from performance degradation. In the current work, we propose hierarchical spatiotemporal graph-regularized correlation filters for robust object tracking. The target sample is decomposed into a large number of deep channels, which are then used to construct a spatial graph such that each graph node corresponds to a particular target location across all channels. Such a graph effectively captures the spatial structure of the target object. In order to capture the temporal structure of the target object, the information in the deep channels obtained from a temporal window is compressed using the principal component analysis, and then, a temporal graph is constructed such that each graph node corresponds to a particular target location in the temporal dimension. Both spatial and temporal graphs span different subspaces such that the target and the background become linearly separable. The learned correlation filter is constrained to act as an eigenvector of the Laplacian of these spatiotemporal graphs. We propose a novel objective function that incorporates these spatiotemporal constraints into the DCFs framework. We solve the objective function using alternating direction methods of multipliers such that each subproblem has a closed-form solution. We evaluate our proposed algorithm on six challenging benchmark datasets and compare it with 33 existing state-of-the art trackers. Our results demonstrate an excellent performance of the proposed algorithm compared to the existing trackers.

Artificial Intelligence-Based Tissue Phenotyping in Colorectal Cancer Histopathology Using Visual and Semantic Features Aggregation

Tissue phenotyping of the tumor microenvironment has a decisive role in digital profiling of intra-tumor heterogeneity, epigenetics, and progression of cancer. Most of the existing methods for tissue phenotyping often rely on time-consuming and error-prone manual procedures. Recently, with the advent of advanced technologies, these procedures have been automated using artificial intelligence techniques. In this paper, a novel deep histology heterogeneous feature aggregation network (HHFA-Net) is proposed based on visual and semantic information fusion for the detection of tissue phenotypes in colorectal cancer (CRC). We adopted and tested various data augmentation techniques to avoid computationally expensive stain normalization procedures and handle limited and imbalanced data problems. Three publicly available datasets are used in the experiments: CRC tissue phenotyping (CRC-TP), CRC histology (CRCH), and colon cancer histology (CCH). The proposed HHFA-Net achieves higher accuracies than the state-of-the-art methods for tissue phenotyping in CRC histopathology images.

Graph Moving Object Segmentation

Moving Object Segmentation (MOS) is a fundamental task in computer vision. Due to undesirable variations in the background scene, MOS becomes very challenging for static and moving camera sequences. Several deep learning methods have been proposed for MOS with impressive performance. However, these methods show performance degradation in the presence of unseen videos; and usually, deep learning models require large amounts of data to avoid overfitting. Recently, graph learning has attracted significant attention in many computer vision applications since they provide tools to exploit the geometrical structure of data. In this work, concepts of graph signal processing are introduced for MOS. First, we propose a new algorithm that is composed of segmentation, background initialization, graph construction, unseen sampling, and a semi-supervised learning method inspired by the theory of recovery of graph signals. Second, theoretical developments are introduced, showing one bound for the sample complexity in semi-supervised learning, and two bounds for the condition number of the Sobolev norm. Our algorithm has the advantage of requiring less labeled data than deep learning methods while having competitive results on both static and moving camera videos. Our algorithm is also adapted for Video Object Segmentation (VOS) tasks and is evaluated on six publicly available datasets outperforming several state-of-the-art methods in challenging conditions.

Spatially Constrained Context-Aware Hierarchical Deep Correlation Filters for Nucleus Detection in Histology Images

Nucleus detection in histology images is a fundamental step for cellular-level analysis in computational pathology. In clinical practice, quantitative nuclear morphology can be used for diagnostic decision making, prognostic stratification, and treatment outcome prediction. Nucleus detection is a challenging task because of large variations in the shape of different types of nucleus such as nuclear clutter, heterogeneous chromatin distribution, and irregular and fuzzy boundaries. To address these challenges, we aim to accurately detect nuclei using spatially constrained context-aware correlation filters using hierarchical deep features extracted from multiple layers of a pre-trained network. During training, we extract contextual patches around each nucleus which are used as negative examples while the actual nucleus patch is used as a positive example. In order to spatially constrain the correlation filters, we propose to construct a spatial structural graph across different nucleus components encoding pairwise similarities. The correlation filters are constrained to act as eigenvectors of the Laplacian of the spatial graphs enforcing these to capture the nucleus structure. A novel objective function is proposed by embedding graph-based structural information as well as the contextual information within the discriminative correlation filter framework. The learned filters are constrained to be orthogonal to both the contextual patches and the spatial graph-Laplacian basis to improve the localization and discriminative performance. The proposed objective function trains a hierarchy of correlation filters on different deep feature layers to capture the heterogeneity in nuclear shape and texture. The proposed algorithm is evaluated on three publicly available datasets and compared with 15 current state-of-the-art methods demonstrating competitive performance in terms of accuracy, speed, and generalization.

Two Ensemble-CNN Approaches for Colorectal Cancer Tissue Type Classification

In recent years, automatic tissue phenotyping has attracted increasing interest in the Digital Pathology (DP) field. For Colorectal Cancer (CRC), tissue phenotyping can diagnose the cancer and differentiate between different cancer grades. The development of Whole Slide Images (WSIs) has provided the required data for creating automatic tissue phenotyping systems. In this paper, we study different hand-crafted feature-based and deep learning methods using two popular multi-classes CRC-tissue-type databases: Kather-CRC-2016 and CRC-TP. For the hand-crafted features, we use two texture descriptors (LPQ and BSIF) and their combination. In addition, two classifiers are used (SVM and NN) to classify the texture features into distinct CRC tissue types. For the deep learning methods, we evaluate four Convolutional Neural Network (CNN) architectures (ResNet-101, ResNeXt-50, Inception-v3, and DenseNet-161). Moreover, we propose two Ensemble CNN approaches: Mean-Ensemble-CNN and NN-Ensemble-CNN. The experimental results show that the proposed approaches outperformed the hand-crafted feature-based methods, CNN architectures and the state-of-the-art methods in both databases.