A machine learning pipeline for supporting differentiation of glioblastomas from single brain metastases

Machine learning has provided, over the last decades, tools for knowledge extraction in complex medical domains. Most of these tools, though, are ad hoc solutions and lack the systematic approach that would be required to become mainstream in medical practice. In this brief paper, we define a machine learning-based analysis pipeline for helping in a difficult problem in the field of neuro-oncology, namely the discrimination of brain glioblastomas from single brain metastases. This pipeline involves source extraction using k-Meansinitialized Convex Non-negative Matrix Factorization and a collection of classifiers, including Logistic Regression, Linear Discriminant Analysis, AdaBoost, and Random Forests.Peer ReviewedPostprint (published version

Detecting adversarial examples with inductive Venn-ABERS predictors

Inductive Venn-ABERS predictors (IVAPs) are a type of probabilistic predictors with the theoretical guarantee that their predictions are perfectly calibrated. We propose to exploit this calibration property for the detection of adversarial examples in binary classification tasks. By rejecting predictions if the uncertainty of the IVAP is too high, we obtain an algorithm that is both accurate on the original test set and significantly more robust to adversarial examples. The method appears to be competitive to the state of the art in adversarial defense, both in terms of robustness as well as scalabilit

Bioinformatics and Medicine in the Era of Deep Learning

Many of the current scientific advances in the life sciences have their origin in the intensive use of data for knowledge discovery. In no area this is so clear as in bioinformatics, led by technological breakthroughs in data acquisition technologies. It has been argued that bioinformatics could quickly become the field of research generating the largest data repositories, beating other data-intensive areas such as high-energy physics or astroinformatics. Over the last decade, deep learning has become a disruptive advance in machine learning, giving new live to the long-standing connectionist paradigm in artificial intelligence. Deep learning methods are ideally suited to large-scale data and, therefore, they should be ideally suited to knowledge discovery in bioinformatics and biomedicine at large. In this brief paper, we review key aspects of the application of deep learning in bioinformatics and medicine, drawing from the themes covered by the contributions to an ESANN 2018 special session devoted to this topic

Bioinformatics and Medicine in the Era of Deep Learning

Many of the current scientific advances in the life sciences have their origin in the intensive use of data for knowledge discovery. In no area this is so clear as in bioinformatics, led by technological breakthroughs in data acquisition technologies. It has been argued that bioinformatics could quickly become the field of research generating the largest data repositories, beating other data-intensive areas such as high-energy physics or astroinformatics. Over the last decade, deep learning has become a disruptive advance in machine learning, giving new live to the long-standing connectionist paradigm in artificial intelligence. Deep learning methods are ideally suited to large-scale data and, therefore, they should be ideally suited to knowledge discovery in bioinformatics and biomedicine at large. In this brief paper, we review key aspects of the application of deep learning in bioinformatics and medicine, drawing from the themes covered by the contributions to an ESANN 2018 special session devoted to this topic

The coming of age of interpretable and explainable machine learning models

Machine learning-based systems are now part of a wide array of real-world applications seamlessly embedded in the social realm. In the wake of this realisation, strict legal regulations for these systems are currently being developed, addressing some of the risks they may pose. This is the coming of age of the interpretability and explainability problems in machine learning-based data analysis, which can no longer be seen just as an academic research problem. In this tutorial, associated to ESANN 2021 special session on “Interpretable Models in Machine Learning and Explainable Artificial Intelligence”, we discuss explainable and interpretable machine learning as post-hoc and ante-hoc strategies to address these problems and highlight several aspects related to them, including their assessment. The contributions accepted for the session are then presented in this contextPeer ReviewedPostprint (published version

Societal issues in machine learning: when learning from data is not enough

It has been argued that Artificial Intelligence (AI) is experiencing a fast process of commodification. Such characterization is on the interest of big IT companies, but it correctly reflects the current industrialization of AI. This phenomenon means that AI systems and products are reaching the society at large and, therefore, that societal issues related to the use of AI and Machine Learning (ML) cannot be ignored any longer. Designing ML models from this human-centered perspective means incorporating human-relevant requirements such as safety, fairness, privacy, and interpretability, but also considering broad societal issues such as ethics and legislation. These are essential aspects to foster the acceptance of ML-based technologies, as well as to ensure compliance with an evolving legislation concerning the impact of digital technologies on ethically and privacy sensitive matters. The ESANN special session for which this tutorial acts as an introduction aims to showcase the state of the art on these increasingly relevant topics among ML theoreticians and practitioners. For this purpose, we welcomed both solid contributions and preliminary relevant results showing the potential, the limitations and the challenges of new ideas, as well as refinements, or hybridizations among the different fields of research, ML and related approaches in facing real-world problems involving societal issues.Peer ReviewedPostprint (published version