Angshuman Paul

Abstract: We propose an improved random forest classifier that performs classification with minimum number of trees. The proposed method iteratively removes some unimportant features. Based on the number of important and unimportant features, we formulate a novel theoretical upper limit on the number of trees to be added to the forest to ensure improvement in classification accuracy. Our algorithm converges with a reduced but important set of features. We prove that further addition of trees or further reduction of features does not improve classification performance. The efficacy of the proposed approach is demonstrated through experiments on benchmark datasets. We further use the proposed classifier to detect mitotic nuclei in the histopathological datasets of breast tissues. We also apply our method on the industrial dataset of dual phase steel microstructures to classify different phases. Results of our method on different datasets show significant reduction in average classification error compared to a number of competing methods.

Abstract: Histopathological grading of cancer not only offers an insight to the patients’ prognosis but also helps in making individual treatment plans. Mitosis counts in histopathological slides play a crucial role for invasive breast cancer grading using the Nottingham grading system. Pathologists perform this grading by manual examinations of a few thousand images for each patient. Hence, finding the mitotic figures from these images is a tedious job and also prone to observer variability due to variations in the appearances of the mitotic cells. We propose a fast and accurate approach for automatic mitosis detection from histopathological images. We employ area morphological scale space for cell segmentation. The scale space is constructed in a novel manner by restricting the scales with the maximization of relative-entropy between the cells and the background. This results in precise cell segmentation. The segmented cells are classified in mitotic and non-mitotic category using the random forest classifier. Experiments show at least 12% improvement in $F_{1}$ score on more than 450 histopathological images at $40\times $ magnification.

Abstract: We propose a fast and accurate method for counting the mitotic figures from histopathological slides using regenerative random forest. Our method performs automatic feature selection in an integrated manner with classification. The proposed random forest assigns a weight to each feature (dimension) of the feature vector in a novel manner based on the importance of the feature (dimension). The forest also assigns a misclassification-based penalty term to each tree in the forest. The trees are then regenerated to make a new population of trees (new forest) and only the more important features survive in the new forest. The feature vector is constructed from domain knowledge using the intensity features of nucleus, features of nuclear membrane and features of the possible stroma region surrounding the cell. The use of domain knowledge improves the classification performance. Experiments show at least 4% improvement in F-measure with an improvement in time complexity on the MITOS dataset from ICPR 2012 grand challenge.

Abstract: Grading of cancer offers insight to the occurrence and progress of the disease. The course of treatment is planned depending on the grade of cancer. Segmentation of the glandular structure of tissue is a prerequisite for grading of colon, prostate and breast cancers. Manual segmentation method is time-consuming and suffers from the curse of observer bias. We propose an automated solution for gland segmentation from hematoxylin & eosin (H&E) stained histology images. Our method relies on the biological cue rather than gland specific signatures that may vary across the slides. We construct a novel informative morphological scale space for gland segmentation. The scale space uses the entropy of the connected components in a novel manner to prevent over segmentation of objects. Our solution is fast, accurate and applicable in a clinical setup. Experiments show an average F1 score of 0.68 for 85 histology images in 20x magnification. We obtain ∼ 30% improvement in F1 score compared to the area morphological scale space method.

Abstract: Proportions of different phases (phase fraction) in the microstructures determine the quality of dual phase (DP) steel. So, calculation of phase fraction in the microstructures of steel samples is important for quality assurance. Manual calculation of phase fraction involves Le Pera etching of steel which is time consuming and dependent on operator efficiency. Calculation of phase fraction from Le Pera etched samples requires cumbersome manual observations. Nital etching is a faster alternative to Le Pera etching. However, due to lack of visually discriminative information, different phases cannot be identified manually from nital images. We propose a novel method for automatic calculation of phase fractions in steel microstructures from nital images using machine learning techniques. We show that regional contour patterns and local entropy (which cannot be evaluated manually) of regions of nital images are related to the formation process of the phases. We design a method that automatically evaluates regional contour patterns and local entropy from nital images of DP steel. Subsequently, we construct a random forest classifier that uses regional contour patterns and local entropy as features for classification of different phases. Our method is ~150 times faster than manual classification. Experiments show close to 90% accuracy in classification.

Abstract: Breast cancer is the most common malignant disease in women worldwide. In recent decades, earlier diagnosis and better adjuvant therapy have substantially improved patient outcome. Diagnosis by histopathology has proven to be instrumental to guide breast cancer treatment, but new challenges have emerged as our increasing understanding of cancer over the years has revealed its complex nature. As patient demand for personalized breast cancer therapy grows, we face an urgent need for more precise biomarker assessment and more accurate histopathologic breast cancer diagnosis to make better therapy decisions. The digitization of pathology data has opened the door to faster, more reproducible, and more precise diagnoses through computerized image analysis. Software to assist diagnostic breast pathology through image processing techniques have been around for years. But recent breakthroughs in artificial intelligence (AI) promise to fundamentally change the way we detect and treat breast cancer in the near future. Machine learning, a subfield of AI that applies statistical methods to learn from data, has seen an explosion of interest in recent years because of its ability to recognize patterns in data with less need for human instruction. One technique in particular, known as deep learning, has produced groundbreaking results in many important problems including image classification and speech recognition. In this review, we will cover the use of AI and deep learning in diagnostic breast pathology, and other recent developments in digital image analysis.

Abstract: Objective: A new image instance segmentation method is proposed to segment individual glands (instances) in colon histology images. This process is challenging since the glands not only need to be segmented from a complex background, they must also be individually identified. Methods: We leverage the idea of image-to-image prediction in recent deep learning by designing an algorithm that automatically exploits and fuses complex multichannel information—regional, location, and boundary cues—in gland histology images. Our proposed algorithm, a deep multichannel framework, alleviates heavy feature design due to the use of convolutional neural networks and is able to meet multifarious requirements by altering channels. Results: Compared with methods reported in the 2015 MICCAI Gland Segmentation Challenge and other currently prevalent instance segmentation methods, we observe state-of-the-art results based on the evaluation metrics. Conclusion: The proposed deep multichannel algorithm is an effective method for gland instance segmentation. Significance: The generalization ability of our model not only enable the algorithm to solve gland instance segmentation problems, but the channel is also alternative that can be replaced for a specific task.

Abstract: Mitosis detection is one of the critical factors of cancer prognosis, carrying significant diagnostic information required for breast cancer grading. It provides vital clues to estimate the aggressiveness and the proliferation rate of the tumour. The manual mitosis quantification from whole slide images is a very labor-intensive and challenging task. The aim of this study is to propose a supervised model to detect mitosis signature from breast histopathology WSI images. The model has been designed using deep learning architecture with handcrafted features. We used handcrafted features issued from previous medical challenges MITOS @ ICPR 2012, AMIDA-13 and projects (MICO ANR TecSan) expertise. The deep learning architecture mainly consists of five convolution layers, four max-pooling layers, four rectified linear units (ReLU), and two fully connected layers. ReLU has been used after each convolution layer as an activation function. Dropout layer has been included after first fully connected layer to avoid overfitting. Handcrafted features mainly consist of morphological, textural and intensity features. The proposed architecture has shown to have an improved 92% precision, 88% recall and 90% F-score. Prospectively, the proposed model will be very beneficial in routine exam, providing pathologists with efficient and - as we will prove - effective second opinion for breast cancer grading from whole slide images. Last but not the least, this model could lead junior and senior pathologists, as medical researchers, to a superior understanding and evaluation of breast cancer stage and genesis.