Correlated product of experts for sparse Gaussian process regression.

Gaussian processes (GPs) are an important tool in machine learning and statistics. However, off-the-shelf GP inference procedures are limited to datasets with several thousand data points because of their cubic computational complexity. For this reason, many sparse GPs techniques have been developed over the past years. In this paper, we focus on GP regression tasks and propose a new approach based on aggregating predictions from several local and correlated experts. Thereby, the degree of correlation between the experts can vary between independent up to fully correlated experts. The individual predictions of the experts are aggregated taking into account their correlation resulting in consistent uncertainty estimates. Our method recovers independent Product of Experts, sparse GP and full GP in the limiting cases. The presented framework can deal with a general kernel function and multiple variables, and has a time and space complexity which is linear in the number of experts and data samples, which makes our approach highly scalable. We demonstrate superior performance, in a time vs. accuracy sense, of our proposed method against state-of-the-art GP approximations for synthetic as well as several real-world datasets with deterministic and stochastic optimization. Supplementary Information: The online version contains supplementary material available at 10.1007/s10994-022-06297-3.

Impact on place of death in cancer patients: a causal exploration in southern Switzerland.

BACKGROUND: Most terminally ill cancer patients prefer to die at home, but a majority die in institutional settings. Research questions about this discrepancy have not been fully answered. This study applies artificial intelligence and machine learning techniques to explore the complex network of factors and the cause-effect relationships affecting the place of death, with the ultimate aim of developing policies favouring home-based end-of-life care. METHODS: A data mining algorithm and a causal probabilistic model for data analysis were developed with information derived from expert knowledge that was merged with data from 116 deceased cancer patients in southern Switzerland. This data set was obtained via a retrospective clinical chart review. RESULTS: Dependencies of disease and treatment-related decisions demonstrate an influence on the place of death of 13%. Anticancer treatment in advanced disease prevents or delays communication about the end of life between oncologists, patients and families. Unknown preferences for the place of death represent a great barrier to a home death. A further barrier is the limited availability of family caregivers for terminal home care. The family's preference for the last place of care has a high impact on the place of death of 51%, while the influence of the patient's preference is low, at 14%. Approximately one-third of family systems can be empowered by health care professionals to provide home care through open end-of-life communication and good symptom management. Such intervention has an influence on the place of death of 17%. If families express a convincing preference for home care, the involvement of a specialist palliative home care service can increase the probability of home deaths by 24%. CONCLUSION: Concerning death at home, open communication about death and dying is essential. Furthermore, for the patient preference for home care to be respected, the family's decision for the last place of care seems to be key. The early initiation of family-centred palliative care and the provision of specialist palliative home care for patients who wish to die at home are suggested.

Reliable survival analysis based on the Dirichlet process.

We present a robust Dirichlet process for estimating survival functions from samples with right-censored data. It adopts a prior near-ignorance approach to avoid almost any assumption about the distribution of the population lifetimes, as well as the need of eliciting an infinite dimensional parameter (in case of lack of prior information), as it happens with the usual Dirichlet process prior. We show how such model can be used to derive robust inferences from right-censored lifetime data. Robustness is due to the identification of the decisions that are prior-dependent, and can be interpreted as an analysis of sensitivity with respect to the hypothetical inclusion of fictitious new samples in the data. In particular, we derive a nonparametric estimator of the survival probability and a hypothesis test about the probability that the lifetime of an individual from one population is shorter than the lifetime of an individual from another. We evaluate these ideas on simulated data and on the Australian AIDS survival dataset. The methods are publicly available through an easy-to-use R package.

Discovering subgroups of patients from DNA copy number data using NMF on compacted matrices.

In the study of complex genetic diseases, the identification of subgroups of patients sharing similar genetic characteristics represents a challenging task, for example, to improve treatment decision. One type of genetic lesion, frequently investigated in such disorders, is the change of the DNA copy number (CN) at specific genomic traits. Non-negative Matrix Factorization (NMF) is a standard technique to reduce the dimensionality of a data set and to cluster data samples, while keeping its most relevant information in meaningful components. Thus, it can be used to discover subgroups of patients from CN profiles. It is however computationally impractical for very high dimensional data, such as CN microarray data. Deciding the most suitable number of subgroups is also a challenging problem. The aim of this work is to derive a procedure to compact high dimensional data, in order to improve NMF applicability without compromising the quality of the clustering. This is particularly important for analyzing high-resolution microarray data. Many commonly used quality measures, as well as our own measures, are employed to decide the number of subgroups and to assess the quality of the results. Our measures are based on the idea of identifying robust subgroups, inspired by biologically/clinically relevance instead of simply aiming at well-separated clusters. We evaluate our procedure using four real independent data sets. In these data sets, our method was able to find accurate subgroups with individual molecular and clinical features and outperformed the standard NMF in terms of accuracy in the factorization fitness function. Hence, it can be useful for the discovery of subgroups of patients with similar CN profiles in the study of heterogeneous diseases.

Reliable diagnoses of dementia by the naive credal classifier inferred from incomplete cognitive data.

Dementia is a serious personal, medical and social problem. Recent research indicates early and accurate diagnoses as the key to effectively cope with it. No definitive cure is available but in some cases when the impairment is still mild the disease can be contained. This paper describes a diagnostic tool that jointly uses the naive credal classifier and the most widely used computerized system of cognitive tests in dementia research, the Cognitive Drug Research system. The naive credal classifier extends the discrete naive Bayes classifier to imprecise probabilities. The naive credal classifier models both prior ignorance and ignorance about the likelihood by sets of probability distributions. This is a new way to deal with small and incomplete datasets that departs significantly from most established classification methods. In the empirical study presented here, the naive credal classifier provides reliability and unmatched predictive performance. It delivers up to 95% correct predictions while being very robust with respect to the partial ignorance due to the largely incomplete data. The diagnostic tool also proves to be very effective in discriminating between Alzheimer's disease and dementia with Lewy bodies.