Semi-Supervised Learning, Causality and the Conditional Cluster Assumption

While the success of semi-supervised learning (SSL) is still not fully understood, Sch\"olkopf et al. (2012) have established a link to the principle of independent causal mechanisms. They conclude that SSL should be impossible when predicting a target variable from its causes, but possible when predicting it from its effects. Since both these cases are somewhat restrictive, we extend their work by considering classification using cause and effect features at the same time, such as predicting disease from both risk factors and symptoms. While standard SSL exploits information contained in the marginal distribution of all inputs (to improve the estimate of the conditional distribution of the target given inputs), we argue that in our more general setting we should use information in the conditional distribution of effect features given causal features. We explore how this insight generalises the previous understanding, and how it relates to and can be exploited algorithmically for SSL.Comment: 36th Conference on Uncertainty in Artificial Intelligence (2020) (Previously presented at the NeurIPS 2019 workshop "Do the right thing": machine learning and causal inference for improved decision making, Vancouver, Canada.

Applicability of semi-supervised learning assumptions for gene ontology terms prediction

Gene Ontology (GO) is one of the most important resources in bioinformatics, aiming to provide a unified framework for the biological annotation of genes and proteins across all species. Predicting GO terms is an essential task for bioinformatics, but the number of available labelled proteins is in several cases insufficient for training reliable machine learning classifiers. Semi-supervised learning methods arise as a powerful solution that explodes the information contained in unlabelled data in order to improve the estimations of traditional supervised approaches. However, semi-supervised learning methods have to make strong assumptions about the nature of the training data and thus, the performance of the predictor is highly dependent on these assumptions. This paper presents an analysis of the applicability of semi-supervised learning assumptions over the specific task of GO terms prediction, focused on providing judgment elements that allow choosing the most suitable tools for specific GO terms. The results show that semi-supervised approaches significantly outperform the traditional supervised methods and that the highest performances are reached when applying the cluster assumption. Besides, it is experimentally demonstrated that cluster and manifold assumptions are complimentary to each other and an analysis of which GO terms can be more prone to be correctly predicted with each assumption, is provided.Postprint (published version

Generative Temporal Models with Spatial Memory for Partially Observed Environments

In model-based reinforcement learning, generative and temporal models of environments can be leveraged to boost agent performance, either by tuning the agent's representations during training or via use as part of an explicit planning mechanism. However, their application in practice has been limited to simplistic environments, due to the difficulty of training such models in larger, potentially partially-observed and 3D environments. In this work we introduce a novel action-conditioned generative model of such challenging environments. The model features a non-parametric spatial memory system in which we store learned, disentangled representations of the environment. Low-dimensional spatial updates are computed using a state-space model that makes use of knowledge on the prior dynamics of the moving agent, and high-dimensional visual observations are modelled with a Variational Auto-Encoder. The result is a scalable architecture capable of performing coherent predictions over hundreds of time steps across a range of partially observed 2D and 3D environments.Comment: ICML 201