Boosting AND/OR-Based Computational Protein Design: Dynamic Heuristics and Generalizable UFO

Scientific computing has experienced a surge empowered by advancements in technologies such as neural networks. However, certain important tasks are less amenable to these technologies, benefiting from innovations to traditional inference schemes. One such task is protein re-design. Recently a new re-design algorithm, AOBB-K*, was introduced and was competitive with state-of-the-art BBK* on small protein re-design problems. However, AOBB-K* did not scale well. In this work we focus on scaling up AOBB-K* and introduce three new versions: AOBB-K*-b (boosted), AOBB-K*-DH (with dynamic heuristics), and AOBB-K*-UFO (with underflow optimization) that significantly enhance scalability.Comment: In proceedings of the 39th Conference on Uncertainty in Artificial Intelligence (UAI 2023) and published in Proceedings of Machine Learning Research (PMLR

Advances in Learning Bayesian Networks of Bounded Treewidth

This work presents novel algorithms for learning Bayesian network structures with bounded treewidth. Both exact and approximate methods are developed. The exact method combines mixed-integer linear programming formulations for structure learning and treewidth computation. The approximate method consists in uniformly sampling $k$-trees (maximal graphs of treewidth $k$), and subsequently selecting, exactly or approximately, the best structure whose moral graph is a subgraph of that $k$-tree. Some properties of these methods are discussed and proven. The approaches are empirically compared to each other and to a state-of-the-art method for learning bounded treewidth structures on a collection of public data sets with up to 100 variables. The experiments show that our exact algorithm outperforms the state of the art, and that the approximate approach is fairly accurate.Comment: 23 pages, 2 figures, 3 table

Adaptive Sampling For Efficient Online Modelling

This thesis examines methods enabling autonomous systems to make active sampling and planning decisions in real time. Gaussian Process (GP) regression is chosen as a framework for its non-parametric approach allowing flexibility in unknown environments. The first part of the thesis focuses on depth constrained full coverage bathymetric surveys in unknown environments. Algorithms are developed to find and follow a depth contour, modelled with a GP, and produce a depth constrained boundary. An extension to the Boustrophedon Cellular Decomposition, Discrete Monotone Polygonal Partitioning is developed allowing efficient planning for coverage within this boundary. Efficient computational methods such as incremental Cholesky updates are implemented to allow online Hyper Parameter optimisation and fitting of the GP's. This is demonstrated in simulation and the field on a platform built for the purpose. The second part of this thesis focuses on modelling the surface salinity profiles of estuarine tidal fronts. The standard GP model assumes evenly distributed noise, which does not always hold. This can be handled with Heteroscedastic noise. An efficient new method, Parametric Heteroscedastic Gaussian Process regression, is proposed. This is applied to active sample selection on stationary fronts and adaptive planning on moving fronts where a number of information theoretic methods are compared. The use of a mean function is shown to increase the accuracy of predictions whilst reducing optimisation time. These algorithms are validated in simulation. Algorithmic development is focused on efficient methods allowing deployment on platforms with constrained computational resources. Whilst the application of this thesis is Autonomous Surface Vessels, it is hoped the issues discussed and solutions provided have relevance to other applications in robotics and wider fields such as spatial statistics and machine learning in general

Active Object Classification from 3D Range Data with Mobile Robots

This thesis addresses the problem of how to improve the acquisition of 3D range data with a mobile robot for the task of object classification. Establishing the identities of objects in unknown environments is fundamental for robotic systems and helps enable many abilities such as grasping, manipulation, or semantic mapping. Objects are recognised by data obtained from sensor observations, however, data is highly dependent on viewpoint; the variation in position and orientation of the sensor relative to an object can result in large variation in the perception quality. Additionally, cluttered environments present a further challenge because key data may be missing. These issues are not always solved by traditional passive systems where data are collected from a fixed navigation process then fed into a perception pipeline. This thesis considers an active approach to data collection by deciding where is most appropriate to make observations for the perception task. The core contributions of this thesis are a non-myopic planning strategy to collect data efficiently under resource constraints, and supporting viewpoint prediction and evaluation methods for object classification. Our approach to planning uses Monte Carlo methods coupled with a classifier based on non-parametric Bayesian regression. We present a novel anytime and non-myopic planning algorithm, Monte Carlo active perception, that extends Monte Carlo tree search to partially observable environments and the active perception problem. This is combined with a particle-based estimation process and a learned observation likelihood model that uses Gaussian process regression. To support planning, we present 3D point cloud prediction algorithms and utility functions that measure the quality of viewpoints by their discriminatory ability and effectiveness under occlusion. The utility of viewpoints is quantified by information-theoretic metrics, such as mutual information, and an alternative utility function that exploits learned data is developed for special cases. The algorithms in this thesis are demonstrated in a variety of scenarios. We extensively test our online planning and classification methods in simulation as well as with indoor and outdoor datasets. Furthermore, we perform hardware experiments with different mobile platforms equipped with different types of sensors. Most significantly, our hardware experiments with an outdoor robot are to our knowledge the first demonstrations of online active perception in a real outdoor environment. Active perception has broad significance in many applications. This thesis emphasises the advantages of an active approach to object classification and presents its assimilation with a wide range of robotic systems, sensors, and perception algorithms. By demonstration of performance enhancements and diversity, our hope is that the concept of considering perception and planning in an integrated manner will be of benefit in improving current systems that rely on passive data collection