arXiv subjects

Paulo J. G. Lisboa

Publications and source records attributed to Paulo J. G. Lisboa.

4 recordsLinked to original sources

arXiv2026

Translation of Black-Box Clinical Prediction Models into Standalone Transparent Nomograms: Temporal External Validation in Heart Transplantation

We convert black-box clinical prediction models for tabular data into standalone nomograms that can be audited term by term. PRiSM (Partial Responses in Structured Models) takes the shape of each effect and interaction from the source model, not merely which variables mattered, and lets the outcome select and weight them. We tested this in 50,356 heart transplant recipients, with validation in a later era than training. Nomograms from all 5 source models - a public clinical risk score, logistic regression, neural networks, random forests and extreme gradient boosting - met a prespecified noninferiority criterion for discrimination before any further simplification, and generally preserved calibration and clinical net benefit. Those from the 3 machine-learning models showed no detectable difference in discrimination from de novo generalized additive and explainable boosting models, exceeded neural additive models, and carried fewer terms than the explainable boosting model. PRiSM is released as an open-source Python package.

cs.LG↗

arXiv2021

The Partial Response Network: a neural network nomogram

Among interpretable machine learning methods, the class of Generalised Additive Neural Networks (GANNs) is referred to as Self-Explaining Neural Networks (SENN) because of the linear dependence on explicit functions of the inputs. In binary classification this shows the precise weight that each input contributes towards the logit. The nomogram is a graphical representation of these weights. We show that functions of individual and pairs of variables can be derived from a functional Analysis of Variance (ANOVA) representation, enabling an efficient feature selection to be carried by application of the logistic Lasso. This process infers the structure of GANNs which otherwise needs to be predefined. As this method is particularly suited for tabular data, it starts by fitting a generic flexible model, in this case a Multi-layer Perceptron (MLP) to which the ANOVA decomposition is applied. This has the further advantage that the resulting GANN can be replicated as a SENN, enabling further refinement of the univariate and bivariate component functions to take place. The component functions are partial responses hence the SENN is a partial response network. The Partial Response Network (PRN) is equally as transparent as a traditional logistic regression model, but capable of non-linear classification with comparable or superior performance to the original MLP. In other words, the PRN is a fully interpretable representation of the MLP, at the level of univariate and bivariate effects. The performance of the PRN is shown to be competitive for benchmark data, against state-of-the-art machine learning methods including GBM, SVM and Random Forests. It is also compared with spline-based Sparse Additive Models (SAM) showing that a semi-parametric representation of the GAM as a neural network can be as effective as the SAM though less constrained by the need to set spline nodes.

cs.LG↗

arXiv2019

A Probabilistic framework for Quantum Clustering

Quantum Clustering is a powerful method to detect clusters in data with mixed density. However, it is very sensitive to a length parameter that is inherent to the Schrödinger equation. In addition, linking data points into clusters requires local estimates of covariance that are also controlled by length parameters. This raises the question of how to adjust the control parameters of the Schrödinger equation for optimal clustering. We propose a probabilistic framework that provides an objective function for the goodness-of-fit to the data, enabling the control parameters to be optimised within a Bayesian framework. This naturally yields probabilities of cluster membership and data partitions with specific numbers of clusters. The proposed framework is tested on real and synthetic data sets, assessing its validity by measuring concordance with known data structure by means of the Jaccard score (JS). This work also proposes an objective way to measure performance in unsupervised learning that correlates very well with JS.

stat.ML↗

arXiv2018

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.

cs.LG↗