Coarse-to-Fine Classification via Parametric and Nonparametric Models for Computer-Aided Diagnosis

Classification is one of the core problems in Computer-Aided Diagnosis (CAD), targeting for early cancer detection using 3D medical imaging interpretation. High detection sensitivity with desirably low false positive (FP) rate is critical for a CAD system to be accepted as a valuable or even indispensable tool in radiologists' workflow. Given various spurious imagery noises which cause observation uncertainties, this remains a very challenging task. In this paper, we propose a novel, two-tiered coarse-to-fine (CTF) classification cascade framework to tackle this problem. We first obtain classification-critical data samples (e.g., samples on the decision boundary) extracted from the holistic data distributions using a robust parametric model (e.g., \cite{Raykar08}); then we build a graph-embedding based nonparametric classifier on sampled data, which can more accurately preserve or formulate the complex classification boundary. These two steps can also be considered as effective "sample pruning" and "feature pursuing + $k$NN/template matching", respectively. Our approach is validated comprehensively in colorectal polyp detection and lung nodule detection CAD systems, as the top two deadly cancers, using hospital scale, multi-site clinical datasets. The results show that our method achieves overall better classification/detection performance than existing state-of-the-art algorithms using single-layer classifiers, such as the support vector machine variants \cite{Wang08}, boosting \cite{Slabaugh10}, logistic regression \cite{Ravesteijn10}, relevance vector machine \cite{Raykar08}, $k$-nearest neighbor \cite{Murphy09} or spectral projections on graph \cite{Cai08}

Improving Computer-aided Detection using Convolutional Neural Networks and Random View Aggregation

Automated computer-aided detection (CADe) in medical imaging has been an important tool in clinical practice and research. State-of-the-art methods often show high sensitivities but at the cost of high false-positives (FP) per patient rates. We design a two-tiered coarse-to-fine cascade framework that first operates a candidate generation system at sensitivities of $\sim$100% but at high FP levels. By leveraging existing CAD systems, coordinates of regions or volumes of interest (ROI or VOI) for lesion candidates are generated in this step and function as input for a second tier, which is our focus in this study. In this second stage, we generate $N$ 2D (two-dimensional) or 2.5D views via sampling through scale transformations, random translations and rotations with respect to each ROI's centroid coordinates. These random views are used to train deep convolutional neural network (ConvNet) classifiers. In testing, the trained ConvNets are employed to assign class (e.g., lesion, pathology) probabilities for a new set of $N$ random views that are then averaged at each ROI to compute a final per-candidate classification probability. This second tier behaves as a highly selective process to reject difficult false positives while preserving high sensitivities. The methods are evaluated on three different data sets with different numbers of patients: 59 patients for sclerotic metastases detection, 176 patients for lymph node detection, and 1,186 patients for colonic polyp detection. Experimental results show the ability of ConvNets to generalize well to different medical imaging CADe applications and scale elegantly to various data sets. Our proposed methods improve CADe performance markedly in all cases. CADe sensitivities improved from 57% to 70%, from 43% to 77% and from 58% to 75% at 3 FPs per patient for sclerotic metastases, lymph nodes and colonic polyps, respectively.Comment: 2D vs 2.5D vs 3D inputs and comparison to other standard classifiers such as SVM have been addressed by more experimentation and two completely new sections and figures. Results and Discussions have been updated accordingl

Deep Convolutional Neural Networks for Computer-Aided Detection: CNN Architectures, Dataset Characteristics and Transfer Learning

Remarkable progress has been made in image recognition, primarily due to the availability of large-scale annotated datasets and the revival of deep CNN. CNNs enable learning data-driven, highly representative, layered hierarchical image features from sufficient training data. However, obtaining datasets as comprehensively annotated as ImageNet in the medical imaging domain remains a challenge. There are currently three major techniques that successfully employ CNNs to medical image classification: training the CNN from scratch, using off-the-shelf pre-trained CNN features, and conducting unsupervised CNN pre-training with supervised fine-tuning. Another effective method is transfer learning, i.e., fine-tuning CNN models pre-trained from natural image dataset to medical image tasks. In this paper, we exploit three important, but previously understudied factors of employing deep convolutional neural networks to computer-aided detection problems. We first explore and evaluate different CNN architectures. The studied models contain 5 thousand to 160 million parameters, and vary in numbers of layers. We then evaluate the influence of dataset scale and spatial image context on performance. Finally, we examine when and why transfer learning from pre-trained ImageNet (via fine-tuning) can be useful. We study two specific computer-aided detection (CADe) problems, namely thoraco-abdominal lymph node (LN) detection and interstitial lung disease (ILD) classification. We achieve the state-of-the-art performance on the mediastinal LN detection, with 85% sensitivity at 3 false positive per patient, and report the first five-fold cross-validation classification results on predicting axial CT slices with ILD categories. Our extensive empirical evaluation, CNN model analysis and valuable insights can be extended to the design of high performance CAD systems for other medical imaging tasks

On conformal divergences and their population minimizers

Total Bregman divergences are a recent tweak of ordinary Bregman divergences originally motivated by applications that required invariance by rotations. They have displayed superior results compared to ordinary Bregman divergences on several clustering, computer vision, medical imaging and machine learning tasks. These preliminary results raise two important problems : First, report a complete characterization of the left and right population minimizers for this class of total Bregman divergences. Second, characterize a principled superset of total and ordinary Bregman divergences with good clustering properties, from which one could tailor the choice of a divergence to a particular application. In this paper, we provide and study one such superset with interesting geometric features, that we call conformal divergences, and focus on their left and right population minimizers. Our results are obtained in a recently coined $(u, v)$-geometric structure that is a generalization of the dually flat affine connections in information geometry. We characterize both analytically and geometrically the population minimizers. We prove that conformal divergences (resp. total Bregman divergences) are essentially exhaustive for their left (resp. right) population minimizers. We further report new results and extend previous results on the robustness to outliers of the left and right population minimizers, and discuss the role of the $(u, v)$-geometric structure in clustering. Additional results are also given

Coarse-to-Fine Curriculum Learning

When faced with learning challenging new tasks, humans often follow sequences of steps that allow them to incrementally build up the necessary skills for performing these new tasks. However, in machine learning, models are most often trained to solve the target tasks directly.Inspired by human learning, we propose a novel curriculum learning approach which decomposes challenging tasks into sequences of easier intermediate goals that are used to pre-train a model before tackling the target task. We focus on classification tasks, and design the intermediate tasks using an automatically constructed label hierarchy. We train the model at each level of the hierarchy, from coarse labels to fine labels, transferring acquired knowledge across these levels. For instance, the model will first learn to distinguish animals from objects, and then use this acquired knowledge when learning to classify among more fine-grained classes such as cat, dog, car, and truck. Most existing curriculum learning algorithms for supervised learning consist of scheduling the order in which the training examples are presented to the model. In contrast, our approach focuses on the output space of the model. We evaluate our method on several established datasets and show significant performance gains especially on classification problems with many labels. We also evaluate on a new synthetic dataset which allows us to study multiple aspects of our method

Coarse-to-Fine Classification via Parametric and Nonparametric Models for Computer-Aided Diagnosis

Classification is one of the core problems in Computer-Aided Diagnosis (CAD), targeting for early cancer detection using 3D medical imaging interpretation. High detection sensitivity with desirably low false positive (FP) rate is critical for a CAD system to be accepted as a valuable or even indispensable tool in radiologists ’ workflow. Given various spurious imagery noises which cause observation uncertainties, this remains a very challenging task. In this paper, we propose a novel, two-tiered coarse-to-fine (CTF) classification cascade framework to tackle this problem. We first obtain classification-critical data samples (e.g., samples on the decision boundary) extracted from the holistic data distributions using a robust parametric model (e.g., [35]); then we build a graph-embedding based nonparametric classifier on sampled data, which can more accurately preserve or formulate the complex classification boundary. These two steps can also be considered as effective “sample pruning ” and “feature pursuing + kNN/template matching”, respectively. Our approach is validated comprehensively in colorectal polyp detection and lung nodule detection CAD systems, as the top two deadly cancers, using hospital scale, multi-site clinical datasets. The results show that our method achieves overall better classification/detection performance than existing state-of-the-art algorithms using single-layer classifiers, such as the support vector machine variants [45], boosting [40], logistic regression [33], relevance vector machine [35], k-nearest neighbor [30] and sparse projections on graph [6]

Coarse-to-Fine Classification via Parametric and Nonparametric Models for Computer-Aided Diagnosis

Classification is one of the core problems in Computer-Aided Diagnosis (CAD), targeting for early cancer detection using 3D medical imaging interpretation. High detection sensitivity with desirably low false positive (FP) rate is critical for a CAD system to be accepted as a valuable or even indispensable tool in radiologists ’ workflow. Given various spurious imagery noises which cause observation uncertainties, this remains a very challenging task. In this paper, we propose a novel, two-tiered coarse-to-fine (CTF) classification cascade framework to tackle this problem. We first obtain classification-critical data samples (e.g., samples on the decision boundary) extracted from the holistic data distributions using a robust parametric model (e.g., [13]); then we build a graph-embedding based nonparametric classifier on sampled data, which can more accurately preserve or formulate the complex classification boundary. These two steps can also be considered as effective “sample pruning ” and “feature pursuing + kNN/template matching”, respectively. Our approach is validated comprehensively in colorectal polyp detection and lung nodule detection CAD systems, as the top two deadly cancers, using hospital scale, multi-site clinical datasets. The results show that our method achieves overall better classification/detection performance than existing state-of-the-art algorithms using single-layer classifiers, such as the support vector machine variants [17], boosting [15], logistic regression [11], relevance vector machine [13], k-nearest neighbor [9] or spectral projections on graph [2]