Controlling False Positive/Negative Rates for Deep-Learning-Based Prostate Cancer Detection on Multiparametric MR images

Prostate cancer (PCa) is one of the leading causes of death for men worldwide. Multi-parametric magnetic resonance (mpMR) imaging has emerged as a non-invasive diagnostic tool for detecting and localising prostate tumours by specialised radiologists. These radiological examinations, for example, for differentiating malignant lesions from benign prostatic hyperplasia in transition zones and for defining the boundaries of clinically significant cancer, remain challenging and highly skill-and-experience-dependent. We first investigate experimental results in developing object detection neural networks that are trained to predict the radiological assessment, using these high-variance labels. We further argue that such a computer-assisted diagnosis (CAD) system needs to have the ability to control the false-positive rate (FPR) or false-negative rate (FNR), in order to be usefully deployed in a clinical workflow, informing clinical decisions without further human intervention. However, training detection networks typically requires a multi-tasking loss, which is not trivial to be adapted for a direct control of FPR/FNR. This work in turn proposes a novel PCa detection network that incorporates a lesion-level cost-sensitive loss and an additional slice-level loss based on a lesion-to-slice mapping function, to manage the lesion- and slice-level costs, respectively. Our experiments based on 290 clinical patients concludes that 1) The lesion-level FNR was effectively reduced from 0.19 to 0.10 and the lesion-level FPR was reduced from 1.03 to 0.66 by changing the lesion-level cost; 2) The slice-level FNR was reduced from 0.19 to 0.00 by taking into account the slice-level cost; (3) Both lesion-level and slice-level FNRs were reduced with lower FP/FPR by changing the lesion-level or slice-level costs, compared with post-training threshold adjustment using networks without the proposed cost-aware training. For the PCa application of interest, the proposed CAD system is capable of substantially reducing FNR with a relatively preserved FPR, therefore is considered suitable for PCa screening applications

Customizing kernel functions for SVM-based hyperspectral image classification

Previous research applying kernel methods such as support vector machines (SVMs) to hyperspectral image classification has achieved performance competitive with the best available algorithms. However, few efforts have been made to extend SVMs to cover the specific requirements of hyperspectral image classification, for example, by building tailor-made kernels. Observation of real-life spectral imagery from the AVIRIS hyperspectral sensor shows that the useful information for classification is not equally distributed across bands, which provides potential to enhance the SVM's performance through exploring different kernel functions. Spectrally weighted kernels are, therefore, proposed, and a set of particular weights is chosen by either optimizing an estimate of generalization error or evaluating each band's utility level. To assess the effectiveness of the proposed method, experiments are carried out on the publicly available 92AV3C dataset collected from the 220-dimensional AVIRIS hyperspectral sensor. Results indicate that the method is generally effective in improving performance: spectral weighting based on learning weights by gradient descent is found to be slightly better than an alternative method based on estimating ";relevance"; between band information and ground trut

Box Drawings for Learning with Imbalanced Data

The vast majority of real world classification problems are imbalanced, meaning there are far fewer data from the class of interest (the positive class) than from other classes. We propose two machine learning algorithms to handle highly imbalanced classification problems. The classifiers constructed by both methods are created as unions of parallel axis rectangles around the positive examples, and thus have the benefit of being interpretable. The first algorithm uses mixed integer programming to optimize a weighted balance between positive and negative class accuracies. Regularization is introduced to improve generalization performance. The second method uses an approximation in order to assist with scalability. Specifically, it follows a \textit{characterize then discriminate} approach, where the positive class is characterized first by boxes, and then each box boundary becomes a separate discriminative classifier. This method has the computational advantages that it can be easily parallelized, and considers only the relevant regions of feature space

Adaptive Learning for the Resource-Constrained Classification Problem

Resource-constrained classification tasks are common in real-world applications such as allocating tests for disease diagnosis, hiring decisions when filling a limited number of positions, and defect detection in manufacturing settings under a limited inspection budget. Typical classification algorithms treat the learning process and the resource constraints as two separate and sequential tasks. Here we design an adaptive learning approach that considers resource constraints and learning jointly by iteratively fine-tuning misclassification costs. Via a structured experimental study using a publicly available data set, we evaluate a decision tree classifier that utilizes the proposed approach. The adaptive learning approach performs significantly better than alternative approaches, especially for difficult classification problems in which the performance of common approaches may be unsatisfactory. We envision the adaptive learning approach as an important addition to the repertoire of techniques for handling resource-constrained classification problems

Imbalanced Deep Learning by Minority Class Incremental Rectification

Model learning from class imbalanced training data is a long-standing and significant challenge for machine learning. In particular, existing deep learning methods consider mostly either class balanced data or moderately imbalanced data in model training, and ignore the challenge of learning from significantly imbalanced training data. To address this problem, we formulate a class imbalanced deep learning model based on batch-wise incremental minority (sparsely sampled) class rectification by hard sample mining in majority (frequently sampled) classes during model training. This model is designed to minimise the dominant effect of majority classes by discovering sparsely sampled boundaries of minority classes in an iterative batch-wise learning process. To that end, we introduce a Class Rectification Loss (CRL) function that can be deployed readily in deep network architectures. Extensive experimental evaluations are conducted on three imbalanced person attribute benchmark datasets (CelebA, X-Domain, DeepFashion) and one balanced object category benchmark dataset (CIFAR-100). These experimental results demonstrate the performance advantages and model scalability of the proposed batch-wise incremental minority class rectification model over the existing state-of-the-art models for addressing the problem of imbalanced data learning.Comment: Accepted for IEEE Trans. Pattern Analysis and Machine Intelligenc

Quality-adjusted survival as an end point in breast cancer trials

Breast cancer treatment recommendations will often require an appraisal of likely benefits in relation to likely side-effects on survival and quality of life (QoL) endpoints, and possibly also an evaluation of the size of the anticipated net clinical benefit against financial costs. Quality-adjusted survival (QAS) analysis methods provide a formal approach for deriving an estimate of net clinical benefit to facilitate this appraisal process. QAS analysis methods have been applied in trials with breast cancer patients of adjuvant therapies as well as treatments for advanced/metastatic disease. QAS analyses based solely on trial data may fail to capture plausible longer-term benefits; thus methods to explore the possible outcomes of treatment beyond the limits of trial data have been developed. These modelling approaches can help researchers gain insights and identify future research priorities, but do not replace the need for long-term evidence from randomised trials.NHMR