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

Case-based decision support system for breast cancer management

Breast cancer is identified as the most common type of cancer in women worldwide with 1.6 million women around the world diagnosed every year. This prompts many active areas of research in identifying better ways to prevent, detect, and treat breast cancer. DESIREE is a European Union funded project, which aims at developing a web-based software ecosystem for the multidisciplinary management of primary breast cancer. The development of an intelligent clinical decision support system offering various modalities of decision support is one of the key objectives of the project. This paper explores case-based reasoning as a problem solving paradigm and discusses the use of an explicit domain knowledge ontology in the development of a knowledge-intensive case-based decision support system for breast cancer management

Improved Heterogeneous Distance Functions

Instance-based learning techniques typically handle continuous and linear input values well, but often do not handle nominal input attributes appropriately. The Value Difference Metric (VDM) was designed to find reasonable distance values between nominal attribute values, but it largely ignores continuous attributes, requiring discretization to map continuous values into nominal values. This paper proposes three new heterogeneous distance functions, called the Heterogeneous Value Difference Metric (HVDM), the Interpolated Value Difference Metric (IVDM), and the Windowed Value Difference Metric (WVDM). These new distance functions are designed to handle applications with nominal attributes, continuous attributes, or both. In experiments on 48 applications the new distance metrics achieve higher classification accuracy on average than three previous distance functions on those datasets that have both nominal and continuous attributes.Comment: See http://www.jair.org/ for an online appendix and other files accompanying this articl

Artificial Intelligence in Radiotherapy Treatment Planning: Present and Future.

Treatment planning is an essential step of the radiotherapy workflow. It has become more sophisticated over the past couple of decades with the help of computer science, enabling planners to design highly complex radiotherapy plans to minimize the normal tissue damage while persevering sufficient tumor control. As a result, treatment planning has become more labor intensive, requiring hours or even days of planner effort to optimize an individual patient case in a trial-and-error fashion. More recently, artificial intelligence has been utilized to automate and improve various aspects of medical science. For radiotherapy treatment planning, many algorithms have been developed to better support planners. These algorithms focus on automating the planning process and/or optimizing dosimetric trade-offs, and they have already made great impact on improving treatment planning efficiency and plan quality consistency. In this review, the smart planning tools in current clinical use are summarized in 3 main categories: automated rule implementation and reasoning, modeling of prior knowledge in clinical practice, and multicriteria optimization. Novel artificial intelligence-based treatment planning applications, such as deep learning-based algorithms and emerging research directions, are also reviewed. Finally, the challenges of artificial intelligence-based treatment planning are discussed for future works

Improving Retrieval Performance of Case Based Reasoning Systems by Fuzzy Clustering

Case-based reasoning (CBR), which is a classical reasoning methodology, has been put to use. Its application has allowed significant progress in resolving problems related to the diagnosis, therapy, and prediction of diseases. However, this methodology has shown some complicated problems that must be resolved, including determining a representation form for the case (complexity, uncertainty, and vagueness of medical information), preventing the case base from the infinite growth of generated medical information and selecting the best retrieval technique. These limitations have pushed researchers to think about other ways of solving problems, and we are recently witnessing the integration of CBR with other techniques such as data mining. In this article, we develop a new approach integrating clustering (Fuzzy C-Means (FCM) and K-Means) in the CBR cycle. Clustering is one of the crucial challenges and has been successfully used in many areas to develop innate structures and hidden patterns for data grouping [1]. The objective of the proposed approach is to solve the limitations of CBR and improve it, particularly in the search for similar cases (retrieval step). The approach is tested with the publicly available immunotherapy dataset. The results of the experimentations show that the integration of the FCM algorithm in the retrieval step reduces the search space (the large volume of information), resolves the problem of the vagueness of medical information, speeds up the calculation and response time, and increases the search efficiency, which further improves the performance of the retrieval step and, consequently, the CBR system

Cluster analysis of the signal curves in perfusion DCE-MRI datasets

Pathological studies show that tumors consist of different sub-regions with more homogeneous vascular properties during their growth. In addition, destroying tumor's blood supply is the target of most cancer therapies. Finding the sub-regions in the tissue of interest with similar perfusion patterns provides us with valuable information about tissue structure and angiogenesis. This information on cancer therapy, for example, can be used in monitoring the response of the cancer treatment to the drug. Cluster analysis of perfusion curves assays to find sub-regions with a similar perfusion pattern. The present work focuses on the cluster analysis of perfusion curves, measured by dynamic contrast enhanced magnetic resonance imaging (DCE-MRI). The study, besides searching for the proper clustering method, follows two other major topics, the choice of an appropriate similarity measure, and determining the number of clusters. These three subjects are connected to each other in such a way that success in one direction will help solving the other problems. This work introduces a new similarity measure, parallelism measure (PM), for comparing the parallelism in the washout phase of the signal curves. Most of the previous works used the Euclidean distance as the measure of dissimilarity. However, the Euclidean distance does not take the patterns of the signal curves into account and therefore for comparing the signal curves is not sufficient. To combine the advantages of both measures a two-steps clustering is developed. The two-steps clustering uses two different similarity measures, the introduced PM measure and Euclidean distance in two consecutive steps. The results of two-steps clustering are compared with the results of other clustering methods. The two-steps clustering besides good performance has some other advantages. The granularity and the number of clusters are controlled by thresholds defined by considering the noise in signal curves. The method is easy to implement and is robust against noise. The focus of the work is mainly the cluster analysis of breast tumors in DCE-MRI datasets. The possibility to adopt the method for liver datasets is studied as well

Defining a robust biological prior from Pathway Analysis to drive Network Inference

Inferring genetic networks from gene expression data is one of the most challenging work in the post-genomic era, partly due to the vast space of possible networks and the relatively small amount of data available. In this field, Gaussian Graphical Model (GGM) provides a convenient framework for the discovery of biological networks. In this paper, we propose an original approach for inferring gene regulation networks using a robust biological prior on their structure in order to limit the set of candidate networks. Pathways, that represent biological knowledge on the regulatory networks, will be used as an informative prior knowledge to drive Network Inference. This approach is based on the selection of a relevant set of genes, called the "molecular signature", associated with a condition of interest (for instance, the genes involved in disease development). In this context, differential expression analysis is a well established strategy. However outcome signatures are often not consistent and show little overlap between studies. Thus, we will dedicate the first part of our work to the improvement of the standard process of biomarker identification to guarantee the robustness and reproducibility of the molecular signature. Our approach enables to compare the networks inferred between two conditions of interest (for instance case and control networks) and help along the biological interpretation of results. Thus it allows to identify differential regulations that occur in these conditions. We illustrate the proposed approach by applying our method to a study of breast cancer's response to treatment