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

Floridoside Extracted from the Red Alga Mastocarpus stellatus Is a Potent Activator of the Classical Complement Pathway

Many biological properties of algae have been found to have useful applications in human health, particularly in the fields of oncology and immunology. Floridoside, extracted from the red alga Mastocarpus stellatus, has a structure similar to the xenoantigen Gal alpha 1–3 Gal. This xenoantigen has been described to induce a high immune response in human xenografts and is mediated by natural anti-gal antibodies that activate the classical complement pathway. Based on this property, we analyzed the potential activities of floridoside on the immune system. We demonstrated that floridoside activates a complement cascade via the classical complement pathway, through the recruitment and activation of natural IgM. This algal molecule could represent an important step in the development of a potent new anticomplementary agent for use in therapeutic complement depletion

Implementing Guideline-based, Experience-based, and Case-based approaches to enrich decision support for the management of breast cancer patients in the DESIREE project

DESIREE is a European-funded project to improve the management of primary breast cancer. We have developed three decision support systems (DSSs), a guideline-based, an experience-based, and a case-based DSSs, resp. GL-DSS, EXP-DSS, and CB-DSS, that operate simultaneously to offer an enriched multi-modal decision support to clinicians. A breast cancer knowledge model has been built to describe within a common ontology the data model and the termino-ontological knowledge used for representing breast cancer patient cases. It allows for rule-based and subsumption-based reasoning in the GL-DSS to provide best patient-centered reconciled care plans. It also allows for using semantic similarity in the retrieval algorithm implemented in the CB-DSS. Rainbow boxes are used to display patient cases similar to a given query patient. This innovative visualization technique translates the question of deciding the most appropriate treatment into a question of deciding the colour dominance among boxes

Exopolysaccharide production by the marine bacterium Alteromonas macleodii Mo169 using fruit pulp waste as the sole carbon source

project LA/P/0140/202019 of the Associate Laboratory Institute for Health and Bioeconomy – i4HB. Publisher Copyright: © 2023 The Author(s)A sugar-rich apple pulp waste generated from fruit processing for juice production was used as the sole carbon source for the cultivation of Alteromonas macleodii Mo169, a marine bacterium known for its EPS-secreting ability. The strain efficiently utilized the glucose and fructose present in the apple pulp waste, reaching biomass and EPS production of 9.20 ± 0.61 and 3.51 ± 0.08 g L−1, respectively, in 24-hour bioreactor cultivation. Two high molecular weight (Mw) fractions (1.7 ± 0.0 and 0.74 ± 0.0 MDa) were detected in the sample recovered from the cell-free supernatant by dialysis. The compositional analysis revealed the presence of glucose (31.1 ± 0.2 mol%), arabinose (23.9 ± 0.1 mol%), mannose (17.3 ± 0.1 mol%), glucosamine (10.3 ± 0.5 mol%), galactose (8.7 ± 0.0 mol%) and galacturonic acid (8.7 ± 0.0 mol%), as well as a high content in sulphate (6.0 ± 0.5 wt%). Given the presence of a high Mw polysaccharide in the apple pulp waste, probably pectin, a fraction of the detected sugar monomers might be attributed to that polymer, which was recovered together with A. macleodii Mo169 EPS. Concomitant with EPS synthesis, there was a viscosity build-up in the cultivation broth, which developed a shear-thinning fluid behaviour not observed in the initial medium. Therefore, this study demonstrates that apple pulp waste can be efficiently converted into a novel polysaccharide by A. macleodii Mo169 in a sustainable bioprocess. Moreover, the EPS sugar and acyl composition, together with its good thickening capacity, render the biopolymer of interest for use in several applications.publishersversionpublishe

Reconciliation of Multiple Guidelines for Decision Support: A case study on the multidisciplinary management of breast cancer within the DESIREE project

Breast cancer is the most common cancer among women. DESIREE is a European project which aims at developing web-based services for the management of primary breast cancer by multidisciplinary breast units (BUs). We describe the guideline-based decision support system (GL-DSS) of the project. Various breast cancer clinical practice guidelines (CPGs) have been selected to be concurrently applied to provide state-of-the-art patient-specific recommendations. The aim is to reconcile CPG recommendations with the objective of complementarity to enlarge the number of clinical situations covered by the GL-DSS. Input and output data exchange with the GL-DSS is performed using FHIR. We used a knowledge model of the domain as an ontology on which relies the reasoning process performed by rules that encode the selected CPGs. Semantic web tools were used, notably the Euler/EYE inference engine, to implement the GL-DSS. "Rainbow boxes" are a synthetic tabular display used to visualize the inferred recommendations

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

Characterisation of Films Based on Exopolysaccharides from Alteromonas Strains Isolated from French Polynesia Marine Environments

LA/P/0140/202019 UID/AGR/04129/2020 LA/P/0037/2020This work assessed the film-forming capacity of exopolysaccharides (EPS) produced by six Alteromonas strains recently isolated from different marine environments in French Polynesia atolls. The films were transparent and resulted in small colour alterations when applied over a coloured surface (ΔEab below 12.6 in the five different colours tested). Moreover, scanning electron microscopy showed that the EPS films were dense and compact, with a smooth surface. High water vapour permeabilities were observed (2.7–6.1 × 10−11 mol m−1 s−1 Pa−1), which are characteristic of hydrophilic polysaccharide films. The films were also characterised in terms of barrier properties to oxygen and carbon dioxide. Interestingly, different behaviours in terms of their mechanical properties under tensile tests were observed: three of the EPS films were ductile with high elongation at break (ε) (35.6–47.0%), low tensile strength at break (Ꞇ) (4.55–11.7 MPa) and low Young’s modulus (εm) (10–93 MPa), whereas the other three were stiffer and more resistant with a higher Ꞇ (16.6–23.6 MPa), lower ε (2.80–5.58%), and higher εm (597–1100 MPa). These properties demonstrate the potential of Alteromonas sp. EPS films to be applied in different areas such as biomedicine, pharmaceuticals, or food packaging.publishersversionpublishe

Biotechnologie des extrêmophiles

En ligne à l'adresse suivante : http://www.techniques-ingenieur.fr/base-documentaire/procedes-chimie-bio-agro-th2/bioprocedes-ti140/biotechnologie-des-extremophiles-bio580