Esther Julien

Giulia Bernardini, Leo van Iersel, Esther Julien et al.

Combining a set of phylogenetic trees into a single phylogenetic network that explains all of them is a fundamental challenge in evolutionary studies. Existing methods are computationally expensive and can either handle only small numbers of phylogenetic trees or are limited to severely restricted classes of networks. In this paper, we apply the recently-introduced theoretical framework of cherry picking to design a class of efficient heuristics that are guaranteed to produce a network containing each of the input trees, for datasets consisting of binary trees. Some of the heuristics in this framework are based on the design and training of a machine learning model that captures essential information on the structure of the input trees and guides the algorithms towards better solutions. We also propose simple and fast randomised heuristics that prove to be very effective when run multiple times. Unlike the existing exact methods, our heuristics are applicable to datasets of practical size, and the experimental study we conducted on both simulated and real data shows that these solutions are qualitatively good, always within some small constant factor from the optimum. Moreover, our machine-learned heuristics are one of the first applications of machine learning to phylogenetics and show its promise.

Justin Dumouchelle, Esther Julien, Jannis Kurtz et al.

Robust optimization is an established framework for modeling optimization problems with uncertain parameters. While static robust optimization is often criticized for being too conservative, two-stage (or adjustable) robust optimization (2RO) provides a less conservative alternative by allowing some decisions to be made after the uncertain parameters have been revealed. Unfortunately, in the case of integer decision variables, existing solution methods for 2RO typically fail to solve large-scale instances, limiting the applicability of this modeling paradigm to simple cases. We propose Neur2RO, a deep-learning-augmented instantiation of the column-and-constraint-generation (CCG) algorithm, which expands the applicability of the 2RO framework to large-scale instances with integer decisions in both stages. A custom-designed neural network is trained to estimate the optimal value and feasibility of the second-stage problem. The network can be incorporated into CCG, leading to more computationally tractable subproblems in each of its iterations. The resulting algorithm enjoys approximation guarantees which depend on the neural network's prediction error. In our experiments, Neur2RO produces high-quality solutions quickly, outperforming state-of-the-art methods on two-stage knapsack, capital budgeting, and facility location problems. Compared to existing methods, which often run for hours, Neur2RO finds better solutions in a few seconds or minutes. Our code is available at https://github.com/khalil-research/Neur2RO.

Esther Julien, Krzysztof Postek, Ş. İlker Birbil

Two-stage robust optimization problems constitute one of the hardest optimization problem classes. One of the solution approaches to this class of problems is K-adaptability. This approach simultaneously seeks the best partitioning of the uncertainty set of scenarios into K subsets, and optimizes decisions corresponding to each of these subsets. In general case, it is solved using the K-adaptability branch-and-bound algorithm, which requires exploration of exponentially-growing solution trees. To accelerate finding high-quality solutions in such trees, we propose a machine learning-based node selection strategy. In particular, we construct a feature engineering scheme based on general two-stage robust optimization insights that allows us to train our machine learning tool on a database of resolved B&B trees, and to apply it as-is to problems of different sizes and/or types. We experimentally show that using our learned node selection strategy outperforms a vanilla, random node selection strategy when tested on problems of the same type as the training problems, also in case the K-value or the problem size differs from the training ones.

Justin Dumouchelle, Esther Julien, Jannis Kurtz et al.

Bilevel optimization deals with nested problems in which a leader takes the first decision to minimize their objective function while accounting for a follower's best-response reaction. Constrained bilevel problems with integer variables are particularly notorious for their hardness. While exact solvers have been proposed for mixed-integer linear bilevel optimization, they tend to scale poorly with problem size and are hard to generalize to the non-linear case. On the other hand, problem-specific algorithms (exact and heuristic) are limited in scope. Under a data-driven setting in which similar instances of a bilevel problem are solved routinely, our proposed framework, Neur2BiLO, embeds a neural network approximation of the leader's or follower's value function, trained via supervised regression, into an easy-to-solve mixed-integer program. Neur2BiLO serves as a heuristic that produces high-quality solutions extremely fast for four applications with linear and non-linear objectives and pure and mixed-integer variables.

Arkadiy Dushatskiy, Esther Julien, Leen Stougie et al.

Tree Containment is a fundamental problem in phylogenetics useful for verifying a proposed phylogenetic network, representing the evolutionary history of certain species. Tree Containment asks whether the given phylogenetic tree (for instance, constructed from a DNA fragment showing tree-like evolution) is contained in the given phylogenetic network. In the general case, this is an NP-complete problem. We propose to solve it approximately using Graph Neural Networks. In particular, we propose to combine the given network and the tree and apply a Graph Neural Network to this network-tree graph. This way, we achieve the capability of solving the tree containment instances representing a larger number of species than the instances contained in the training dataset (i.e., our algorithm has the inductive learning ability). Our algorithm demonstrates an accuracy of over $95\%$ in solving the tree containment problem on instances with up to 100 leaves.