Protein subcellular localization is an important factor in normal cellular processes and disease. While many protein localization resources treat it as static, protein localization is dynamic and heavily influenced by biological context. Biological pathways are graphs that represent a specific biological context and can be inferred from large-scale data. We develop graph algorithms to predict the localization of all interactions in a biological pathway as an edge-labeling task. We compare a variety of models including graph neural networks, probabilistic graphical models, and discriminative classifiers for predicting localization annotations from curated pathway databases. We also perform a case study where we construct biological pathways and predict localizations of human fibroblasts undergoing viral infection. Pathway localization prediction is a promising approach for integrating publicly available localization data into the analysis of large-scale biological data.

Estimating information-theoretic quantities such as entropy and mutual information is central to many problems in statistics and machine learning, but challenging in high dimensions. This paper presents estimators of entropy via inference (EEVI), which deliver upper and lower bounds on many information quantities for arbitrary variables in a probabilistic generative model. These estimators use importance sampling with proposal distribution families that include amortized variational inference and sequential Monte Carlo, which can be tailored to the target model and used to squeeze true information values with high accuracy. We present several theoretical properties of EEVI and demonstrate scalability and efficacy on two problems from the medical domain: (i) in an expert system for diagnosing liver disorders, we rank medical tests according to how informative they are about latent diseases, given a pattern of observed symptoms and patient attributes; and (ii) in a differential equation model of carbohydrate metabolism, we find optimal times to take blood glucose measurements that maximize information about a diabetic patient's insulin sensitivity, given their meal and medication schedule.

We develop an optimization algorithm suitable for Bayesian learning in complex models. Our approach relies on natural gradient updates within a general black-box framework for efficient training with limited model-specific derivations. It applies within the class of exponential-family variational posterior distributions, for which we extensively discuss the Gaussian case for which the updates have a rather simple form. Our Quasi Black-box Variational Inference (QBVI) framework is readily applicable to a wide class of Bayesian inference problems and is of simple implementation as the updates of the variational posterior do not involve gradients with respect to the model parameters, nor the prescription of the Fisher information matrix. We develop QBVI under different hypotheses for the posterior covariance matrix, discuss details about its robust and feasible implementation, and provide a number of real-world applications to demonstrate its effectiveness.

Recently, we have been witnesses of accidents involving autonomous vehicles and their lack of sufficient information. One way to tackle this issue is to benefit from the perception of different view points, namely cooperative perception. We propose here a decentralized collaboration, i.e. peer-to-peer, in which the agents are active in their quest for full perception by asking for specific areas in their surroundings on which they would like to know more. Ultimately, we want to optimize a trade-off between the maximization of knowledge about moving objects and the minimization of the total volume of information received from others, to limit communication costs and message processing time. For this, we propose a way to learn a communication policy that reverses the usual communication paradigm by only requesting from other vehicles what is unknown to the ego-vehicle, instead of filtering on the sender side. We tested three different generative models to be taken as base for a Deep Reinforcement Learning (DRL) algorithm, and compared them to a broadcasting policy and a policy randomly selecting areas. In particular, we propose Locally Predictable VAE (LP-VAE), which appears to be producing better belief states for predictions than state-of-the-art models, both as a standalone model and in the context of DRL. Experiments were conducted in the driving simulator CARLA. Our best models reached on average a gain of 25% of the total complementary information, while only requesting about 5% of the ego-vehicle's perceptual field. This trade-off is adjustable through the interpretable hyperparameters of our reward function.

Shannon information was defined for characterizing the uncertainty information of classical probabilistic distributions. As an uncertainty measure it is generally believed to be positive. This holds for any information quantity from two random variables because of the polymatroidal axioms. However, it is unknown why there is negative information for more than two random variables on finite dimensional spaces. We first show the negative tripartite Shannon mutual information implies specific Bayesian network representations of its joint distribution. We then show that the negative Shannon information is obtained from general tripartite Bayesian networks with quantum realizations. This provides a device-independent witness of negative Shannon information. We finally extend the result for general networks. The present result shows new insights in the network compatibility from non-Shannon information inequalities.

Causal discovery for quantitative data has been extensively studied but less is known for categorical data. We propose a novel causal model for categorical data based on a new classification model, termed classification with optimal label permutation (COLP). By design, COLP is a parsimonious classifier, which gives rise to a provably identifiable causal model. A simple learning algorithm via comparing likelihood functions of causal and anti-causal models suffices to learn the causal direction. Through experiments with synthetic and real data, we demonstrate the favorable performance of the proposed COLP-based causal model compared to state-of-the-art methods. We also make available an accompanying R package COLP, which contains the proposed causal discovery algorithm and a benchmark dataset of categorical cause-effect pairs.

A machine learning (ML) system must learn not only to match the output of a target function on a training set, but also to generalize to novel situations in order to yield accurate predictions at deployment. In most practical applications, the user cannot exhaustively enumerate every possible input to the model; strong generalization performance is therefore crucial to the development of ML systems which are performant and reliable enough to be deployed in the real world. While generalization is well-understood theoretically in a number of hypothesis classes, the impressive generalization performance of deep neural networks has stymied theoreticians. In deep reinforcement learning (RL), our understanding of generalization is further complicated by the conflict between generalization and stability in widely-used RL algorithms. This thesis will provide insight into generalization by studying the learning dynamics of deep neural networks in both supervised and reinforcement learning tasks.

Monitoring and managing Earth's forests in an informed manner is an important requirement for addressing challenges like biodiversity loss and climate change. While traditional in situ or aerial campaigns for forest assessments provide accurate data for analysis at regional level, scaling them to entire countries and beyond with high temporal resolution is hardly possible. In this work, we propose a method based on deep ensembles that densely estimates forest structure variables at country-scale with 10-meter resolution, using freely available satellite imagery as input. Our method jointly transforms Sentinel-2 optical images and Sentinel-1 synthetic-aperture radar images into maps of five different forest structure variables: 95th height percentile, mean height, density, Gini coefficient, and fractional cover. We train and test our model on reference data from 41 airborne laser scanning missions across Norway and demonstrate that it is able to generalize to unseen test regions, achieving normalized mean absolute errors between 11% and 15%, depending on the variable. Our work is also the first to propose a variant of so-called Bayesian deep learning to densely predict multiple forest structure variables with well-calibrated uncertainty estimates from satellite imagery. The uncertainty information increases the trustworthiness of the model and its suitability for downstream tasks that require reliable confidence estimates as a basis for decision making. We present an extensive set of experiments to validate the accuracy of the predicted maps as well as the quality of the predicted uncertainties. To demonstrate scalability, we provide Norway-wide maps for the five forest structure variables.

Abstract: A persistent challenge in conditional image synthesis has been to generate diverse output images from the same input image despite only one output image being observed per input image. GAN-based methods are prone to mode collapse, which leads to low diversity. To get around this, we leverage Implicit Maximum Likelihood Estimation (IMLE) which can overcome mode collapse fundamentally. IMLE uses the same generator as GANs but trains it with a different, non-adversarial objective which ensures each observed image has a generated sample nearby. Unfortunately, to generate high-fidelity images, prior IMLE-based methods require a large number of samples, which is expensive.

The energy consumption of private households amounts to approximately 30% of the total global energy consumption, causing a large share of the CO2 emissions through energy production. An intelligent demand response via load shifting increases the energy efficiency of residential buildings by nudging residents to change their energy consumption behavior. This paper introduces an activity prediction-based framework for the utility-based context-aware multi-agent recommendation system that generates an activity shifting schedule for a 24-hour time horizon to either focus on CO2 emissions or energy cost savings. In particular, we design and implement an Activity Agent that uses hourly energy consumption data. It does not require further sensorial data or activity labels which reduces implementation costs and the need for extensive user input. Moreover, the system enhances the utility option of saving energy costs by saving CO2 emissions and provides the possibility to focus on both dimensions. The empirical results show that while setting the focus on CO2 emissions savings, the system provides an average of 12% of emissions savings and 7% of cost savings. When focusing on energy cost savings, 20% of energy costs and 6% of emissions savings are possible for the studied households in case of accepting all recommendations. Recommending an activity schedule, the system uses the same terms residents describe their domestic life. Therefore, recommendations can be more easily integrated into daily life supporting the acceptance of the system in a long-term perspective.