Explainable artificial intelligence for breast cancer: A visual case-based reasoning approach

International audienceCase-Based Reasoning (CBR) is a form of analogical reasoning in which the solution for a (new) query case is determined using a database of previous known cases with their solutions. Cases similar to the query are retrieved from the database, and then their solutions are adapted to the query. In medicine, a case usually corresponds to a patient and the problem consists of classifying the patient in a class of diagnostic or therapy. Compared to "black box" algorithms such as deep learning, the responses of CBR systems can be justified easily using the similar cases as examples. However, this possibility is often under-exploited and the explanations provided by most CBR systems are limited to the display of the similar cases. In this paper, we propose a CBR method that can be both executed automatically as an algorithm and presented visually in a user interface for providing visual explanations or for visual reasoning. After retrieving similar cases, a visual interface displays quantitative and qualitative similarities between the query and the similar cases, so as one can easily classify the query through visual reasoning, in a fully explainable manner. It combines a quantitative approach (visualized by a scatter plot based on Multidimensional Scaling in polar coordinates , preserving distances involving the query) and a qualitative approach (set visualization using rainbow boxes). We applied this method to breast cancer management. We showed on three public datasets that our qualitative method has a classification accuracy comparable to k-Nearest Neighbors algorithms, but is better explainable. We also tested the proposed interface during a small user study. Finally, we apply the proposed approach to a real dataset in breast cancer. Medical experts found the visual approach interesting as it explains why cases are similar through the visualization of shared patient characteristics

How Fitch-Margoliash Algorithm can Benefit from Multi Dimensional Scaling

Whatever the phylogenetic method, genetic sequences are often described as strings of characters, thus molecular sequences can be viewed as elements of a multi-dimensional space. As a consequence, studying motion in this space (ie, the evolutionary process) must deal with the amazing features of high-dimensional spaces like concentration of measured phenomenon

Exploration of High-dimensional Scalar Function for Nuclear Reactor Safety Analysis and Visualization: A User's Guide to TopoXG*

Large-scale simulation datasets can be modeled as high-dimensional scalar functions defined over a discrete sample of the domain. The goals of our proposed research are two-fold. First, we would like to provide structural analysis of a function at multiple scales and provide insight into the relationship between the input parameters and the output. Second, we enable exploratory analysis for users, where we help the users to differentiate features from noise through multi-scale analysis on an interactive platform, based on domain knowledge and data characterization. TopoXG is a software package that is designed to address these goals. The unique contribution of TopoXG lies in exploiting the topological and geometric properties of the domain, building statistical models based on its topological segmentations and providing interactive visual interfaces to facilitate such explorations. We provide a user’s guide to TopoXG, by highlighting its analysis and visualization capabilities, and giving several use cases involving datasets from nuclear reactor safety simulations

Faithful visualization and dimensionality reduction on graphics processing unit

Information visualization is a process of transforming data, information and knowledge to the geometric representation in order to see unseen information. Dimensionality reduction (DR) is one of the strategies used to visualize high-dimensional data sets by projecting them onto low-dimensional space where they can be visualized directly. The problem of DR is that the straightforward relationship between the original highdimensional data sets and low-dimensional space is lost, which causes the colours of visualization to have no meaning. A new nonlinear DR method which is called faithful stochastic proximity embedding (FSPE) is proposed in this thesis to visualize more complex data sets. The proposed method depends on the low-dimensional space rather than the high-dimensional data sets to overcome the main shortcomings of the DR by overcoming the false neighbour points, and preserving the neighbourhood relation to the true neighbours. The visualization by our proposed method displays the faithful, useful and meaningful colours, where the objects of the image can be easily distinguished. The experiments that were conducted indicated that the FSPE is higher in accuracy than many dimension reduction methods because it prevents as much as possible the false neighbourhood errors to occur in the results. In addition, in the results of other methods, we have demonstrated that the FSPE has an important role in enhancing the low-dimensional space which are carried by other DR methods. Choosing the worst efficient points to update the rest of the points has helped in improving the visualization information. The results showed the proposed method has an impacting role in increasing the trustworthiness of the visualization by retrieving most of the local neighbourhood points, which they missed during the projection process. The sequential dimensionality reduction (SDR) method is the second proposed method in this thesis. It redefines the problem of DR as a sequence of multiple DR problems, each of which reduces the dimensionality by a small amount. It maintains and preserves the relations among neighbour points in low-dimensional space. The results showed the accuracy of the proposed SDR, which leads to a better visualization with minimum false colours compared to the direct projection of the DR method, where those results are confirmed by comparing our method with 21 other methods. Although there are many measurement metrics, our proposed point-wise correlation metric is the better. In this metric, we evaluate the efficiency of each point in the visualization to generate a grey-scale efficiency image. This type of image gives more details instead of representing the evaluation in one single value. The user can recognize the location of both the false and the true points. We compared the results of our proposed methods (FSPE and SDR) and many other dimension reduction methods when applied to four scenarios: (1) the unfolding curved cylinder data sets; (2) projecting a human face data sets into two dimensions; (3) classifing connected networks and (4) visualizing a remote sensing imagery data sets. The results showed that our methods are able to produce good visualization by preserving the corresponding colour distances between the visualization and the original data sets. The proposed methods are implemented on the graphic processing unit (GPU) to visualize different data sets. The benefit of a parallel implementation is to obtain the results in as short a time as possible. The results showed that compute unified device architecture (CUDA) implementation of FSPE and SDR are faster than their sequential codes on the central processing unit (CPU) in calculating floating-point operations, especially for a large data sets. The GPU is also more suited to the implementation of the metric measurement methods because they do a large computation. We illustrated that this massive speed-up requires a parallel structure to be suitable for running on a GPU

Visualization of high-dimensional data with relational perspective map

Abstract This paper introduces a method called relational perspective map (RPM) to visualize distance information in high-dimensional spaces. Like conventional multidimensional scaling, the RPM algorithm aims to produce proximity preserving 2-dimensional (2-D) maps. The main idea of the RPM algorithm is to simulate a multiparticle system on a closed surface: whereas the repulsive forces between the particles reflect the distance information, the closed surface holds the whole system in balance and prevents the resulting map from degeneracy. A special feature of RPM algorithm is its ability to partition a complex dataset into pieces and map them onto a 2-D space without overlapping. Compared to other multidimensional scaling methods, RPM is able to reveal more local details of complex datasets. This paper demonstrates the properties of RPM maps with four examples and provides extensive comparison to other multidimensional scaling methods, such as Sammon Mapping and Curvilinear Principle Analysis

Visualization of High-Dimensional Data With Relational Perspective Map

This paper introduces a method called relational perspective map (RPM) to visualize distance information in high-dimensional spaces. Like conventional multidimensional scaling, the RPM algorithm aims to produce proximity preserving 2-dimensional (2-D) maps. The main idea of the RPM algorithm is to simulate a multiparticle system on a closed surface: whereas the repulsive forces between the particles reflect the distance information, the closed surface holds the whole system in balance and prevents the resulting map from degeneracy. A special feature of RPM algorithm is its ability to partition a complex dataset into pieces and map them onto a 2-D space without overlapping. Compared to other multidimensional scaling methods, RPM is able to reveal more local details of complex datasets. This paper demonstrates the properties of RPM maps with four examples and provides extensive comparison to other multidimensional scaling methods, such as Sammon Mapping and Curvilinear Principle Analysis