Cancer diagnosis using deep learning: A bibliographic review

In this paper, we first describe the basics of the field of cancer diagnosis, which includes steps of cancer diagnosis followed by the typical classification methods used by doctors, providing a historical idea of cancer classification techniques to the readers. These methods include Asymmetry, Border, Color and Diameter (ABCD) method, seven-point detection method, Menzies method, and pattern analysis. They are used regularly by doctors for cancer diagnosis, although they are not considered very efficient for obtaining better performance. Moreover, considering all types of audience, the basic evaluation criteria are also discussed. The criteria include the receiver operating characteristic curve (ROC curve), Area under the ROC curve (AUC), F1 score, accuracy, specificity, sensitivity, precision, dice-coefficient, average accuracy, and Jaccard index. Previously used methods are considered inefficient, asking for better and smarter methods for cancer diagnosis. Artificial intelligence and cancer diagnosis are gaining attention as a way to define better diagnostic tools. In particular, deep neural networks can be successfully used for intelligent image analysis. The basic framework of how this machine learning works on medical imaging is provided in this study, i.e., pre-processing, image segmentation and post-processing. The second part of this manuscript describes the different deep learning techniques, such as convolutional neural networks (CNNs), generative adversarial models (GANs), deep autoencoders (DANs), restricted Boltzmann’s machine (RBM), stacked autoencoders (SAE), convolutional autoencoders (CAE), recurrent neural networks (RNNs), long short-term memory (LTSM), multi-scale convolutional neural network (M-CNN), multi-instance learning convolutional neural network (MIL-CNN). For each technique, we provide Python codes, to allow interested readers to experiment with the cited algorithms on their own diagnostic problems. The third part of this manuscript compiles the successfully applied deep learning models for different types of cancers. Considering the length of the manuscript, we restrict ourselves to the discussion of breast cancer, lung cancer, brain cancer, and skin cancer. The purpose of this bibliographic review is to provide researchers opting to work in implementing deep learning and artificial neural networks for cancer diagnosis a knowledge from scratch of the state-of-the-art achievements

Image segmentation in the wavelet domain using N-cut framework

We introduce a wavelet domain image segmentation algorithm based on Normalized Cut (NCut) framework in this thesis. By employing the NCut algorithm we solve the perceptual grouping problem of image segmentation which aims at the extraction of the global impression of an image. We capitalize on the reduced set of data to be processed and statistical features derived from the wavelet-transformed images to solve graph partitioning more efficiently than before. Five orientation histograms are computed to evaluate similarity/dissimilarity measure of local structure. We use properties of the wavelet transform filtering to capture edge information in vertical, horizontal and diagonal orientations. This approach allows for direct processing of compressed data and results in faster implementation of NCut framework than that in the spatial domain and also decent quality of segmentation of natural scene images

Multi-Modality Automatic Lung Tumor Segmentation Method Using Deep Learning and Radiomics

Delineation of the tumor volume is the initial and fundamental step in the radiotherapy planning process. The current clinical practice of manual delineation is time-consuming and suffers from observer variability. This work seeks to develop an effective automatic framework to produce clinically usable lung tumor segmentations. First, to facilitate the development and validation of our methodology, an expansive database of planning CTs, diagnostic PETs, and manual tumor segmentations was curated, and an image registration and preprocessing pipeline was established. Then a deep learning neural network was constructed and optimized to utilize dual-modality PET and CT images for lung tumor segmentation. The feasibility of incorporating radiomics and other mechanisms such as a tumor volume-based stratification scheme for training/validation/testing were investigated to improve the segmentation performance. The proposed methodology was evaluated both quantitatively with similarity metrics and clinically with physician reviews. In addition, external validation with an independent database was also conducted. Our work addressed some of the major limitations that restricted clinical applicability of the existing approaches and produced automatic segmentations that were consistent with the manually contoured ground truth and were highly clinically-acceptable according to both the quantitative and clinical evaluations. Both novel approaches of implementing a tumor volume-based training/validation/ testing stratification strategy as well as incorporating voxel-wise radiomics feature images were shown to improve the segmentation performance. The results showed that the proposed method was effective and robust, producing automatic lung tumor segmentations that could potentially improve both the quality and consistency of manual tumor delineation

Evaluating indoor positioning systems in a shopping mall : the lessons learned from the IPIN 2018 competition

The Indoor Positioning and Indoor Navigation (IPIN) conference holds an annual competition in which indoor localization systems from different research groups worldwide are evaluated empirically. The objective of this competition is to establish a systematic evaluation methodology with rigorous metrics both for real-time (on-site) and post-processing (off-site) situations, in a realistic environment unfamiliar to the prototype developers. For the IPIN 2018 conference, this competition was held on September 22nd, 2018, in Atlantis, a large shopping mall in Nantes (France). Four competition tracks (two on-site and two off-site) were designed. They consisted of several 1 km routes traversing several floors of the mall. Along these paths, 180 points were topographically surveyed with a 10 cm accuracy, to serve as ground truth landmarks, combining theodolite measurements, differential global navigation satellite system (GNSS) and 3D scanner systems. 34 teams effectively competed. The accuracy score corresponds to the third quartile (75th percentile) of an error metric that combines the horizontal positioning error and the floor detection. The best results for the on-site tracks showed an accuracy score of 11.70 m (Track 1) and 5.50 m (Track 2), while the best results for the off-site tracks showed an accuracy score of 0.90 m (Track 3) and 1.30 m (Track 4). These results showed that it is possible to obtain high accuracy indoor positioning solutions in large, realistic environments using wearable light-weight sensors without deploying any beacon. This paper describes the organization work of the tracks, analyzes the methodology used to quantify the results, reviews the lessons learned from the competition and discusses its future

Hypothesis-based image segmentation for object learning and recognition

Denecke A. Hypothesis-based image segmentation for object learning and recognition. Bielefeld: Universität Bielefeld; 2010.This thesis addresses the figure-ground segmentation problem in the context of complex systems for automatic object recognition as well as for the online and interactive acquisition of visual representations. First the problem of image segmentation in general terms and next its importance for object learning in current state-of-the-art systems is introduced. Secondly a method using artificial neural networks is presented. This approach on the basis of Generalized Learning Vector Quantization is investigated in challenging scenarios such as the real-time figure-ground segmentation of complex shaped objects under continuously changing environment conditions. The ability to fulfill these requirements characterizes the novelty of the approach compared to state-of-the-art methods. Finally our technique is extended towards online adaption of model complexity and the integration of several segmentation cues. This yields a framework for object segmentation that is applicable to improve current systems for visual object learning and recognition

Chronology of brain tumor classification of intelligent systems based on mathematical modeling, simulation and image processing techniques

Tumor classification using image processing techniques is becoming a powerful tool nowadays. Based on the importance of this technique, the motivation of this review paper is to present the chronology of brain tumor classification using the digital images and govern the mathematical modeling and simulation of intelligent systems. The intelligent system involves artificial neural network (ANN), fuzzy logic (FL), support vector machine (SVM), and parallel support vector machine (PSVM). The chronology of brain tumor classification presents the latest part of the literature reviews related to the principal, type and interpretation of segmentation and classification of brain tumors via the large digital dataset from magnetic resonance imaging (MRI) images. This paper has been classified the modeling and simulation in classical and automatic models. Around 115 literature reviews in high ranking journal and high citation index are referred. This paper contains 6 contents, including mathematical modeling, numerical simulation, image processing, numerical results and performance, lastly is the conclusion to standardize the frame concept for the future of chronological framework involving the mathematical modeling and simulation. Research outcome to differentiate the tumor classification based on MRI images, modeling and simulation. Future work outlier in segmentation and classification are given in conclusion

Novel Image Markers for Non-Small Cell Lung Cancer Classification and Survival Prediction

BACKGROUND: Non-small cell lung cancer (NSCLC), the most common type of lung cancer, is one of serious diseases causing death for both men and women. Computer-aided diagnosis and survival prediction of NSCLC, is of great importance in providing assistance to diagnosis and personalize therapy planning for lung cancer patients. RESULTS: In this paper we have proposed an integrated framework for NSCLC computer-aided diagnosis and survival analysis using novel image markers. The entire biomedical imaging informatics framework consists of cell detection, segmentation, classification, discovery of image markers, and survival analysis. A robust seed detection-guided cell segmentation algorithm is proposed to accurately segment each individual cell in digital images. Based on cell segmentation results, a set of extensive cellular morphological features are extracted using efficient feature descriptors. Next, eight different classification techniques that can handle high-dimensional data have been evaluated and then compared for computer-aided diagnosis. The results show that the random forest and adaboost offer the best classification performance for NSCLC. Finally, a Cox proportional hazards model is fitted by component-wise likelihood based boosting. Significant image markers have been discovered using the bootstrap analysis and the survival prediction performance of the model is also evaluated. CONCLUSIONS: The proposed model have been applied to a lung cancer dataset that contains 122 cases with complete clinical information. The classification performance exhibits high correlations between the discovered image markers and the subtypes of NSCLC. The survival analysis demonstrates strong prediction power of the statistical model built from the discovered image markers

Optimal Multi-Stage Arrhythmia Classification Approach

Arrhythmia constitutes a problem with the rate or rhythm of the heartbeat, and an early diagnosis is essential for the timely inception of successful treatment. We have jointly optimized the entire multi-stage arrhythmia classification scheme based on 12-lead surface ECGs that attains the accuracy performance level of professional cardiologists. The new approach is comprised of a three-step noise reduction stage, a novel feature extraction method and an optimal classification model with finely tuned hyperparameters. We carried out an exhaustive study comparing thousands of competing classification algorithms that were trained on our proprietary, large and expertly labeled dataset consisting of 12-lead ECGs from 40,258 patients with four arrhythmia classes: atrial fibrillation, general supraventricular tachycardia, sinus bradycardia and sinus rhythm including sinus irregularity rhythm. Our results show that the optimal approach consisted of Low Band Pass filter, Robust LOESS, Non Local Means smoothing, a proprietary feature extraction method based on percentiles of the empirical distribution of ratios of interval lengths and magnitudes of peaks and valleys, and Extreme Gradient Boosting Tree classifier, achieved an F1-Score of 0.988 on patients without additional cardiac conditions. The same noise reduction and feature extraction methods combined with Gradient Boosting Tree classifier achieved an F1-Score of 0.97 on patients with additional cardiac conditions. Our method achieved the highest classification accuracy (average 10-fold cross-validation F1-Score of 0.992) using an external validation data, MIT-BIH arrhythmia database. The proposed optimal multi-stage arrhythmia classification approach can dramatically benefit automatic ECG data analysis by providing cardiologist level accuracy and robust compatibility with various ECG data sources