Non-negative Subspace Feature Representation for Few-shot Learning in Medical Imaging

Unlike typical visual scene recognition domains, in which massive datasets are accessible to deep neural networks, medical image interpretations are often obstructed by the paucity of data. In this paper, we investigate the effectiveness of data-based few-shot learning in medical imaging by exploring different data attribute representations in a low-dimensional space. We introduce different types of non-negative matrix factorization (NMF) in few-shot learning, addressing the data scarcity issue in medical image classification. Extensive empirical studies are conducted in terms of validating the effectiveness of NMF, especially its supervised variants (e.g., discriminative NMF, and supervised and constrained NMF with sparseness), and the comparison with principal component analysis (PCA), i.e., the collaborative representation-based dimensionality reduction technique derived from eigenvectors. With 14 different datasets covering 11 distinct illness categories, thorough experimental results and comparison with related techniques demonstrate that NMF is a competitive alternative to PCA for few-shot learning in medical imaging, and the supervised NMF algorithms are more discriminative in the subspace with greater effectiveness. Furthermore, we show that the part-based representation of NMF, especially its supervised variants, is dramatically impactful in detecting lesion areas in medical imaging with limited samples.

Thinking Outside the Box: Orthogonal Approach to Equalizing Protected Attributes

There is growing concern that the potential of black box AI may exacerbate health-related disparities and biases such as gender and ethnicity in clinical decision-making. Biased decisions can arise from data availability and collection processes, as well as from the underlying confounding effects of the protected attributes themselves. This work proposes a machine learning-based orthogonal approach aiming to analyze and suppress the effect of the confounder through discriminant dimensionality reduction and orthogonalization of the protected attributes against the primary attribute information. By doing so, the impact of the protected attributes on disease diagnosis can be realized, undesirable feature correlations can be mitigated, and the model prediction performance can be enhanced.

IIHT: Medical Report Generation with Image-to-Indicator Hierarchical Transformer

Automated medical report generation has become increasingly important in medical analysis. It can produce computer-aided diagnosis descriptions and thus significantly alleviate the doctors' work. Inspired by the huge success of neural machine translation and image captioning, various deep learning methods have been proposed for medical report generation. However, due to the inherent properties of medical data, including data imbalance and the length and correlation between report sequences, the generated reports by existing methods may exhibit linguistic fluency but lack adequate clinical accuracy. In this work, we propose an image-to-indicator hierarchical transformer (IIHT) framework for medical report generation. It consists of three modules, i.e., a classifier module, an indicator expansion module and a generator module. The classifier module first extracts image features from the input medical images and produces disease-related indicators with their corresponding states. The disease-related indicators are subsequently utilised as input for the indicator expansion module, incorporating the "data-text-data" strategy. The transformer-based generator then leverages these extracted features along with image features as auxiliary information to generate final reports. Furthermore, the proposed IIHT method is feasible for radiologists to modify disease indicators in real-world scenarios and integrate the operations into the indicator expansion module for fluent and accurate medical report generation. Extensive experiments and comparisons with state-of-the-art methods under various evaluation metrics demonstrate the great performance of the proposed method.

Proximal nested sampling with data-driven priors for physical scientists

Proximal nested sampling was introduced recently to open up Bayesian model selection for high-dimensional problems such as computational imaging. The framework is suitable for models with a log-convex likelihood, which are ubiquitous in the imaging sciences. The purpose of this article is two-fold. First, we review proximal nested sampling in a pedagogical manner in an attempt to elucidate the framework for physical scientists. Second, we show how proximal nested sampling can be extended in an empirical Bayes setting to support data-driven priors, such as deep neural networks learned from training data.

Semantic Segmentation by Semantic Proportions

Semantic segmentation is a critical task in computer vision that aims to identify and classify individual pixels in an image, with numerous applications for example autonomous driving and medical image analysis. However, semantic segmentation can be super challenging particularly due to the need for large amounts of annotated data. Annotating images is a time-consuming and costly process, often requiring expert knowledge and significant effort. In this paper, we propose a novel approach for semantic segmentation by eliminating the need of ground-truth segmentation maps. Instead, our approach requires only the rough information of individual semantic class proportions, shortened as semantic proportions. It greatly simplifies the data annotation process and thus will significantly reduce the annotation time and cost, making it more feasible for large-scale applications. Moreover, it opens up new possibilities for semantic segmentation tasks where obtaining the full ground-truth segmentation maps may not be feasible or practical. Extensive experimental results demonstrate that our approach can achieve comparable and sometimes even better performance against the benchmark method that relies on the ground-truth segmentation maps. Utilising semantic proportions suggested in this work offers a promising direction for future research in the field of semantic segmentation.

GO-LDA: Generalised Optimal Linear Discriminant Analysis

Linear discriminant analysis (LDA) has been a useful tool in pattern recognition and data analysis research and practice. While linearity of class boundaries cannot always be expected, nonlinear projections through pre-trained deep neural networks have served to map complex data onto feature spaces in which linear discrimination has served well. The solution to binary LDA is obtained by eigenvalue analysis of within-class and between-class scatter matrices. It is well known that the multiclass LDA is solved by an extension to the binary LDA, a generalised eigenvalue problem, from which the largest subspace that can be extracted is of dimension one lower than the number of classes in the given problem. In this paper, we show that, apart from the first of the discriminant directions, the generalised eigenanalysis solution to multiclass LDA does neither yield orthogonal discriminant directions nor maximise discrimination of projected data along them. Surprisingly, to the best of our knowledge, this has not been noted in decades of literature on LDA. To overcome this drawback, we present a derivation with a strict theoretical support for sequentially obtaining discriminant directions that are orthogonal to previously computed ones and maximise in each step the Fisher criterion. We show distributions of projections along these axes and demonstrate that discrimination of data projected onto these discriminant directions has optimal separation, which is much higher than those from the generalised eigenvectors of the multiclass LDA. Using a wide range of benchmark tasks, we present a comprehensive empirical demonstration that on a number of pattern recognition and classification problems, the optimal discriminant subspaces obtained by the proposed method, referred to as GO-LDA (Generalised Optimal LDA), can offer superior accuracy.

3D Orientation Field Transform

The two-dimensional (2D) orientation field transform has been proved to be effective at enhancing 2D contours and curves in images by means of top-down processing. It, however, has no counterpart in three-dimensional (3D) images due to the extremely complicated orientation in 3D compared to 2D. Practically and theoretically, the demand and interest in 3D can only be increasing. In this work, we modularise the concept and generalise it to 3D curves. Different modular combinations are found to enhance curves to different extents and with different sensitivity to the packing of the 3D curves. In principle, the proposed 3D orientation field transform can naturally tackle any dimensions. As a special case, it is also ideal for 2D images, owning simpler methodology compared to the previous 2D orientation field transform. The proposed method is demonstrated with several transmission electron microscopy tomograms ranging from 2D curve enhancement to, the more important and interesting, 3D ones.

A Two-stage Classification Method for High-dimensional Data and Point Clouds

High-dimensional data classification is a fundamental task in machine learning and imaging science. In this paper, we propose a two-stage multiphase semi-supervised classification method for classifying high-dimensional data and unstructured point clouds. To begin with, a fuzzy classification method such as the standard support vector machine is used to generate a warm initialization. We then apply a two-stage approach named SaT (smoothing and thresholding) to improve the classification. In the first stage, an unconstraint convex variational model is implemented to purify and smooth the initialization, followed by the second stage which is to project the smoothed partition obtained at stage one to a binary partition. These two stages can be repeated, with the latest result as a new initialization, to keep improving the classification quality. We show that the convex model of the smoothing stage has a unique solution and can be solved by a specifically designed primal-dual algorithm whose convergence is guaranteed. We test our method and compare it with the state-of-the-art methods on several benchmark data sets. The experimental results demonstrate clearly that our method is superior in both the classification accuracy and computation speed for high-dimensional data and point clouds.

Three-dimensional Segmentation of Trees Through a Flexible Multi-Class Graph Cut Algorithm (MCGC)

Developing a robust algorithm for automatic individual tree crown (ITC) detection from laser scanning datasets is important for tracking the responses of trees to anthropogenic change. Such approaches allow the size, growth and mortality of individual trees to be measured, enabling forest carbon stocks and dynamics to be tracked and understood. Many algorithms exist for structurally simple forests including coniferous forests and plantations. Finding a robust solution for structurally complex, species-rich tropical forests remains a challenge; existing segmentation algorithms often perform less well than simple area-based approaches when estimating plot-level biomass. Here we describe a Multi-Class Graph Cut (MCGC) approach to tree crown delineation. This uses local three-dimensional geometry and density information, alongside knowledge of crown allometries, to segment individual tree crowns from LiDAR point clouds. Our approach robustly identifies trees in the top and intermediate layers of the canopy, but cannot recognise small trees. From these three-dimensional crowns, we are able to measure individual tree biomass. Comparing these estimates to those from permanent inventory plots, our algorithm is able to produce robust estimates of hectare-scale carbon density, demonstrating the power of ITC approaches in monitoring forests. The flexibility of our method to add additional dimensions of information, such as spectral reflectance, make this approach an obvious avenue for future development and extension to other sources of three-dimensional data, such as structure from motion datasets.

Linkage between Piecewise Constant Mumford-Shah model and ROF model and its virtue in image segmentation

The piecewise constant Mumford-Shah (PCMS) model and the Rudin-Osher-Fatemi (ROF) model are two of the most famous variational models in image segmentation and image restoration, respectively. They have ubiquitous applications in image processing. In this paper, we explore the linkage between these two important models. We prove that for two-phase segmentation problem the optimal solution of the PCMS model can be obtained by thresholding the minimizer of the ROF model. This linkage is still valid for multiphase segmentation under mild assumptions. Thus it opens a new segmentation paradigm: image segmentation can be done via image restoration plus thresholding. This new paradigm, which circumvents the innate non-convex property of the PCMS model, therefore improves the segmentation performance in both efficiency (much faster than state-of-the-art methods based on PCMS model, particularly when the phase number is high) and effectiveness (producing segmentation results with better quality) due to the flexibility of the ROF model in tackling degraded images, such as noisy images, blurry images or images with information loss. As a by-product of the new paradigm, we derive a novel segmentation method, coined thresholded-ROF (T-ROF) method, to illustrate the virtue of manipulating image segmentation through image restoration techniques. The convergence of the T-ROF method under certain conditions is proved, and elaborate experimental results and comparisons are presented.