Binary phylogenetic trees inferred from biological data are central to understanding the shared evolutionary history of organisms. Inferring the placement of latent nodes in a tree by any optimality criterion (e.g., maximum likelihood) is an NP-hard problem, propelling the development of myriad heuristic approaches. Yet, these heuristics often lack a systematic means of uniformly sampling random trees or effectively exploring a tree space that grows factorially, which are crucial to optimisation problems such as machine learning. Phylo2Vec maps any binary tree with n leaves to an integer vector of length n 1. We prove that Phylo2Vec is both well-defined and bijective to the space of phylogenetic trees. The advantages of Phylo2Vec are twofold: i) easy uniform sampling of binary trees and ii) systematic ability to traverse tree space in very large or small jumps. As a proof of concept, we use Phylo2Vec for maximum likelihood inference on five real-world datasets and show that a simple hill climbing-based optimisation can efficiently traverse the vastness of tree space from a random to an optimal tree. Phylogenetic trees are a fundamental tool in depicting evolutionary processes, whether linguistic (evolution of different languages and language families) or biological (evolution of biological entities). In the latter field, phylogenetic trees are integral to multiple research domains, including evolution (Morlon et al., 2010), conservation (Rolland et al., 2011), and epidemiology, where they allow us to better understand infectious disease transmission dynamics (Ypma et al., 2013; Faria et al., 2021). A multitude of computer-readable formats have been proposed to store and represent (binary) phylogenetic trees. While basic data structures such as arrays or linked lists can be used for this purpose, the Newick format, as outlined by Olsen (1990) and Felsenstein (2004), has emerged as the standard notation. Each parenthesis encloses a pair of leaf nodes or subtrees, separated by a comma.

Training neural networks that require adversarial optimization, such as generative adversarial networks (GANs) and unsupervised domain adaptations (UDAs), suffers from instability. This instability problem comes from the difficulty of the minimax optimization, and there have been various approaches in GANs and UDAs to overcome this problem. In this study, we tackle this problem theoretically through a functional analysis. Specifically, we show the convergence property of the minimax problem by the gradient descent over the infinite-dimensional spaces of continuous functions and probability measures under certain conditions. Using this setting, we can discuss GANs and UDAs comprehensively, which have been studied independently. In addition, we show that the conditions necessary for the convergence property are interpreted as stabilization techniques of adversarial training such as the spectral normalization and the gradient penalty.

Meta-learning is a powerful approach that exploits historical data to quickly solve new tasks from the same distribution. In the low-data regime, methods based on the closed-form posterior of Gaussian processes (GP) together with Bayesian optimization have achieved high performance. However, these methods are either computationally expensive or introduce assumptions that hinder a principled propagation of uncertainty between task models. This may disrupt the balance between exploration and exploitation during optimization. In this paper, we develop ScaML-GP, a modular GP model for meta-learning that is scalable in the number of tasks. Our core contribution is a carefully designed multi-task kernel that enables hierarchical training and task scalability. Conditioning ScaML-GP on the meta-data exposes its modular nature yielding a test-task prior that combines the posteriors of meta-task GPs. In synthetic and real-world meta-learning experiments, we demonstrate that ScaML-GP can learn efficiently both with few and many meta-tasks.

In this paper, we put forth a novel framework (named ``RYU'') for the construction of ``safe'' balls, i.e. regions that provably contain the dual solution of a target optimization problem. We concentrate on the standard setup where the cost function is the sum of two terms: a closed, proper, convex Lipschitz-smooth function and a closed, proper, convex function. The RYU framework is shown to generalize or improve upon all the results proposed in the last decade for the considered family of optimization problems.

Humanitarian logistics operations face increasing difficulties due to rising demands for aid in disaster areas. This paper investigates the dynamic allocation of scarce relief supplies across multiple affected districts over time. It introduces a novel stochastic dynamic post-disaster inventory allocation problem with trucks and unmanned aerial vehicles delivering relief goods under uncertain supply and demand. The relevance of this humanitarian logistics problem lies in the importance of considering the inter-temporal social impact of deliveries. We achieve this by incorporating deprivation costs when allocating scarce supplies. Furthermore, we consider the inherent uncertainties of disaster areas and the potential use of cargo UAVs to enhance operational efficiency. This study proposes two anticipatory solution methods based on approximate dynamic programming, specifically decomposed linear value function approximation and neural network value function approximation to effectively manage uncertainties in the dynamic allocation process. We compare DL-VFA and NN-VFA with various state-of-the-art methods (exact re-optimization, PPO) and results show a 6-8% improvement compared to the best benchmarks. NN-VFA provides the best performance and captures nonlinearities in the problem, whereas DL-VFA shows excellent scalability against a minor performance loss. The experiments reveal that consideration of deprivation costs results in improved allocation of scarce supplies both across affected districts and over time. Finally, results show that deploying UAVs can play a crucial role in the allocation of relief goods, especially in the first stages after a disaster. The use of UAVs reduces transportation- and deprivation costs together by 16-20% and reduces maximum deprivation times by 19-40%, while maintaining similar levels of demand coverage, showcasing efficient and effective operations.

Our work presents a novel approach to shape optimization, with the twofold objective to improve the efficiency of global optimization algorithms while promoting the generation of high-quality designs during the optimization process free of geometrical anomalies. This is accomplished by reducing the number of the original design variables defining a new reduced subspace where the geometrical variance is maximized and modeling the underlying generative process of the data via probabilistic linear latent variable models such as factor analysis and probabilistic principal component analysis. We show that the data follows approximately a Gaussian distribution when the shape modification method is linear and the design variables are sampled uniformly at random, due to the direct application of the central limit theorem. The degree of anomalousness is measured in terms of Mahalanobis distance, and the paper demonstrates that abnormal designs tend to exhibit a high value of this metric. This enables the definition of a new optimization model where anomalous geometries are penalized and consequently avoided during the optimization loop. The procedure is demonstrated for hull shape optimization of the DTMB 5415 model, extensively used as an international benchmark for shape optimization problems. The global optimization routine is carried out using Bayesian optimization and the DIRECT algorithm. From the numerical results, the new framework improves the convergence of global optimization algorithms, while only designs with high-quality geometrical features are generated through the optimization routine thereby avoiding the wastage of precious computationally expensive simulations.

In this paper, we present a bilevel optimal motion planning (BOMP) model for autonomous parking. The BOMP model treats motion planning as an optimal control problem, in which the upper level is designed for vehicle nonlinear dynamics, and the lower level is for geometry collision-free constraints. The significant feature of the BOMP model is that the lower level is a linear programming problem that serves as a constraint for the upper-level problem. That is, an optimal control problem contains an embedded optimization problem as constraints. Traditional optimal control methods cannot solve the BOMP problem directly. Therefore, the modified approximate Karush-Kuhn-Tucker theory is applied to generate a general nonlinear optimal control problem. Then the pseudospectral optimal control method solves the converted problem. Particularly, the lower level is the $J_2$-function that acts as a distance function between convex polyhedron objects. Polyhedrons can approximate vehicles in higher precision than spheres or ellipsoids. Besides, the modified $J_2$-function (MJ) and the active-points based modified $J_2$-function (APMJ) are proposed to reduce the variables number and time complexity. As a result, an iteirative two-stage BOMP algorithm for autonomous parking concerning dynamical feasibility and collision-free property is proposed. The MJ function is used in the initial stage to find an initial collision-free approximate optimal trajectory and the active points, then the APMJ function in the final stage finds out the optimal trajectory. Simulation results and experiment on Turtlebot3 validate the BOMP model, and demonstrate that the computation speed increases almost two orders of magnitude compared with the area criterion based collision avoidance method.

Quantum Annealers (QAs) operate as single-instruction machines, lacking a SWAP operation to overcome limited qubit connectivity. Consequently, multiple physical qubits are chained to form a program qubit with higher connectivity, resulting in a drastically diminished effective QA capacity by up to 33x. We observe that in QAs: (a) chain lengths exhibit a power-law distribution, a few dominant chains holding substantially more qubits than others; and (b) about 25% of physical qubits remain unused, getting isolated between these chains. We propose Skipper, a software technique that enhances the capacity and fidelity of QAs by skipping dominant chains and substituting their program qubit with two readout results. Using a 5761-qubit QA, we demonstrate that Skipper can tackle up to 59% (Avg. 28%) larger problems when eleven chains are skipped. Additionally, Skipper can improve QA fidelity by up to 44% (Avg. 33%) when cutting five chains (32 runs). Users can specify up to eleven chain cuts in Skipper, necessitating about 2,000 distinct quantum executable runs. To mitigate this, we introduce Skipper-G, a greedy scheme that skips sub-problems less likely to hold the global optimum, executing a maximum of 23 quantum executables with eleven chain trims. Skipper-G can boost QA fidelity by up to 41% (Avg. 29%) when cutting five chains (11 runs).

Artificial intelligence (AI) technology has become increasingly prevalent and transforms our everyday life. One important application of AI technology is the development of autonomous vehicles (AV). However, the reliability of an AV needs to be carefully demonstrated via an assurance test so that the product can be used with confidence in the field. To plan for an assurance test, one needs to determine how many AVs need to be tested for how many miles and the standard for passing the test. Existing research has made great efforts in developing reliability demonstration tests in the other fields of applications for product development and assessment. However, statistical methods have not been utilized in AV test planning. This paper aims to fill in this gap by developing statistical methods for planning AV reliability assurance tests based on recurrent events data. We explore the relationship between multiple criteria of interest in the context of planning AV reliability assurance tests. Specifically, we develop two test planning strategies based on homogeneous and non-homogeneous Poisson processes while balancing multiple objectives with the Pareto front approach. We also offer recommendations for practical use. The disengagement events data from the California Department of Motor Vehicles AV testing program is used to illustrate the proposed assurance test planning methods.

In this survey, we offer an extensive overview of the Online Influence Maximization (IM) problem by covering both theoretical aspects and practical applications. For the integrity of the article and because the online algorithm takes an offline oracle as a subroutine, we first make a clear definition of the Offline IM problem and summarize those commonly used Offline IM algorithms, which include traditional approximation or heuristic algorithms and ML-based algorithms. Then, we give a standard definition of the Online IM problem and a basic Combinatorial Multi-Armed Bandit (CMAB) framework, CMAB-T. Here, we summarize three types of feedback in the CMAB model and discuss in detail how to study the Online IM problem based on the CMAB-T model. This paves the way for solving the Online IM problem by using online learning methods. Furthermore, we have covered almost all Online IM algorithms up to now, focusing on characteristics and theoretical guarantees of online algorithms for different feedback types. Here, we elaborately explain their working principle and how to obtain regret bounds. Besides, we also collect plenty of innovative ideas about problem definition and algorithm designs and pioneering works for variants of the Online IM problem and their corresponding algorithms. Finally, we encapsulate current challenges and outline prospective research directions from four distinct perspectives.