Optimal Tree Research Articles

Phylogenetic tree instability after taxon addition: empirical frequency, predictability, and consequences for online inference.

Online phylogenetic inference methods add sequentially arriving sequences to an inferred phylogeny without the need to recompute the entire tree from scratch. Some online method implementations exist already, but there remains concern that additional sequences may change the topological relationship among the original set of taxa. We call such a change in tree topology a lack of stability for the inferred tree. In this paper, we analyze the stability of single taxon addition in a Maximum Likelihood framework across 1, 000 empirical datasets. We find that instability occurs in almost 90% of our examples, although observed topological differences do not always reach significance under the AU-test. Changes in tree topology after addition of a taxon rarely occur close to its attachment location, and are more frequently observed in more distant tree locations carrying low bootstrap support. To investigate whether instability is predictable, we hypothesize sources of instability and design summary statistics addressing these hypotheses. Using these summary statistics as input features for machine learning under random forests, we are able to predict instability and can identify the most influential features. In summary, it does not appear that a strict insertion-only online inference method will deliver globally optimal trees, although relaxing insertion strictness by allowing for a small number of final tree rearrangements or accepting slightly suboptimal solutions appears feasible.

Improved survival prediction for kidney transplant outcomes using artificial intelligence-based models: development of the UK Deceased Donor Kidney Transplant Outcome Prediction (UK-DTOP) Tool

The UK Deceased Donor Kidney Transplant Outcome Prediction (UK-DTOP) Tool, developed using advanced artificial intelligence (AI), significantly enhances the prediction of outcomes for deceased-donor kidney transplants in the UK. This study analyzed data from the UK Transplant Registry (UKTR), including 29,713 transplant cases between 2008 and 2022, to assess the predictive performance of three machine learning models: XGBoost, Random Survival Forest, and Optimal Decision Tree. Among these, XGBoost demonstrated exceptional performance with the highest concordance index of 0.74 and an area under the curve (AUC) consistently above 0.73, indicating robust discriminative ability and calibration. In comparison to the traditional Kidney Donor Risk Index (KDRI), which achieved a lower concordance index of 0.57, the UK-DTOP model marked a significant improvement, underscoring its superior predictive accuracy. The advanced capabilities of the XGBoost model were further highlighted through calibration assessments using the Integrated Brier Score (IBS), showing a score of 0.14, indicative of precise survival probability predictions. Additionally, unsupervised learning via k-means clustering was employed to identify five distinct clusters based on donor and transplant characteristics, uncovering nuanced insights into graft survival outcomes. These clusters were further analyzed using Bayesian Cox regression, which confirmed significant survival outcome variations across the clusters, thereby validating the model’s effectiveness in enhancing risk stratification. The UK-DTOP tool offers a comprehensive decision-support system that significantly refines pre-transplant decision-making. The study’s findings advocate for the adoption of AI-enhanced tools in healthcare systems to optimize organ matching and transplant success, potentially guiding future developments in global transplant practices.

Gentrius: generating trees compatible with a set of unrooted subtrees and its application to phylogenetic terraces.

For a set of binary unrooted subtrees generating all binary unrooted trees compatible with them, i.e. generating their stand, is one of the classical problems in phylogenetics. Here, we introduce Gentrius - an efficient algorithm to tackle this task. The algorithm has a direct application in practice. Namely, Gentrius generates phylogenetic terraces - topologically distinct, equally scoring trees due to missing data. Despite stand generation being computationally intractable, we showed on simulated and biological datasets that Gentrius generates stands with millions of trees in feasible time. We exemplify that depending on the distribution of missing data across species and loci and the inferred phylogeny, the number of equally optimal terrace trees varies tremendously. The strict consensus tree computed from them displays all the branches unaffected by the pattern of missing data. Thus, by solving the problem of stand generation, in practice Gentrius provides an important systematic assessment of phylogenetic trees inferred from incomplete data. Furthermore, Gentrius can aid theoretical research by fostering understanding of tree space structure imposed by missing data.

Associations between an open-response situational judgment test and performance on OSCEs and fieldwork: implications for admissions decisions and matriculant diversity in an occupational therapy program

BackgroundCasper, an online open-response situational judgement test that assesses social intelligence and professionalism [1], is used in admissions to health professions programs.MethodThis study (1) explored the incremental validity of Casper over grade point average (GPA) for predicting student performance on objective structured clinical examinations (OSCEs) and fieldwork placements within an occupational therapy program, (2) examined optimal weighting of Casper in GPA in admissions decisions using non-linear optimization and regression tree analysis to find the weights associated with the highest average competency scores, and (3) investigated whether Casper could be used to impact the diversity of a cohort selected for admission to the program.ResultsMultiple regression analysis results indicate that Casper improves the prediction of OSCE and fieldwork performance over and above GPA (change in Adj. R2 = 3.2%). Non-linear optimization and regression tree analysis indicate the optimal weights of GPA and Casper for predicting performance across fieldwork placements are 0.16 and 0.84, respectively. Furthermore, the findings suggest that students with a slightly lower GPA (e.g., 3.5–3.6) could be successful in the program as assessed by fieldwork, which is considered to be the strongest indicator of success as an entry-level clinician. In terms of diversity, no statistically significant differences were found between those actually admitted and those who would have been admitted using Casper.ConclusionThese results constitute preliminary validity evidence supporting the integration of Casper into applicant selection in an occupational therapy graduate program.

Approximating decision trees with priority hypotheses

This paper addresses the problem of creating decision trees for identifying hypotheses, also known as entities, in a setting where the cost of an action is dependent on the true hypothesis. Specifically, we consider the scenario where n hypotheses are divided into m groups based on their priority levels. Taking an action on a higher priority hypothesis incurs a higher cost. This is relevant to many real-world applications where cost-sensitive decisions need to be made. For example, in a medical diagnosis task, the goal is to take a series of actions (such as medical tests) to identify a cause. Each action in this process requires conducting a test on the patient and observing the outcome, which can take anywhere from a few minutes to several weeks depending on the test. In this case, the cost (the result of waiting for the outcome) is higher if the true hypothesis is more time-sensitive. For example, if the true hypothesis is toxic chemical exposure (as opposed to a chronic disease such as diabetes), a delay of a few minutes could significantly increase the patient's risk of mortality. We propose a group greedy algorithm to solve this problem. We demonstrate that under worst-case scenarios, our algorithm has an approximation ratio of O(mlog⁡n). Importantly, when m=1, meaning there is only one group of hypotheses, our result is consistent with the logarithmic approximation bound for the traditional optimal decision tree problem.

Policy Learning for Many Outcomes of Interest: Combining Optimal Policy Trees with Multi-objective Bayesian Optimisation

AbstractMethods for learning optimal policies use causal machine learning models to create human-interpretable rules for making choices around the allocation of different policy interventions. However, in realistic policy-making contexts, decision-makers often care about trade-offs between outcomes, not just single-mindedly maximising utility for one outcome. This paper proposes an approach termed Multi-Objective Policy Learning (MOPoL) which combines optimal decision trees for policy learning with a multi-objective Bayesian optimisation approach to explore the trade-off between multiple outcomes. It does this by building a Pareto frontier of non-dominated models for different hyperparameter settings which govern outcome weighting. The method is applied to a real-world case-study of pricing targetting subsididies for anti-malarial medication in Kenya.

Site-based climate-smart tree species selection for forestation under climate change

Global climate change threatens ecosystem functions and resilience, prompting large-scale planting initiatives to mitigate its impacts. To ensure new plantations are adaptive to future climates, it is crucial to consider climate mismatches resulting from climate change when selecting tree species. However, current research is all species-based, which is not effective for species selection across species at specific plantation sites. Our research developed a novel site-based approach that can identify optimal tree species for specific planting sites under projected future climates. We evaluated the feasibility and effectiveness of this method across 10 representative sites in diverse climatic zones in China based on climate niche projections for 100 key tree species. Our findings demonstrated the necessity and effectiveness of this approach, which can select a suit of suitable tree species tailored for any potential planting site across China under different climate change scenarios. For instance, at Tibet Dongjiu Forest farm, Aibes densa and Quercus pannosa currently showed high suitability scores above 0.8 (on a scale of 0–1). However, by the 2080s, Aibes densa's suitability was projected to drop to 0.25, while Quercus pannosa was expected to maintain its suitability. Conversely, Quercus aquifolioides currently had a low suitability of 0.08, but it was projected to increase to 0.74 by the 2080s. These findings demonstrate the importance of using this approach to avoid selecting the wrong species or overlooking potentially suitable species. In addition, our simulation analysis suggests that a dataset of 40–50 species is necessary to ensure that most planting sites can identify 2–3 suitable species. This advancement significantly enhances the precision and effectiveness of tree species selection strategies for local practitioners, offering vital insights for forestry, conservation, and ecological restoration projects. These results highlight the tremendous potential and practical applicability of our site-based approach in enhancing forestry adaptation and ecological functions in response to global climate change.

GIS-based management of a campus tree inventory for assessing optimal shade tree locations: a case study of National Cheng Kung University, Taiwan

GIS-based management of a campus tree inventory for assessing optimal shade tree locations: a case study of National Cheng Kung University, Taiwan

Abstract P102: Reducing Testing Burden in Patients Screened for Primary Aldosteronism

Introduction: Primary aldosteronism (PA) is an increasingly recognized secondary cause of hypertension characterized by higher cardiovascular, renal, and metabolic disease rates than blood pressure-matched essential hypertensives. Current literature suggests expanding screening for PA to include the majority, if not all, hypertensive patients. This expansive screening would place considerable burden on patients and the healthcare system. A simple clinical risk prediction model that identifies patients with low risk for PA could reduce this testing burden. Methods: We evaluated 111 hypertensive patients in the Southern Illinois University Hypertension Clinic who underwent a screening test and, if positive, had subsequent confirmatory testing for PA. We characterized patients based on routine clinical measures including antihypertensive treatment intensity, blood pressure, serum electrolytes, and body size. Classification trees incorporating 96 patients without missing data points for any considered predictor variable were used to identify hypertensive screen-positive patients who have low to absent risk for PA as determined by confirmatory testing. Results: Patients with PA had higher serum aldosterone levels at screening (mean = 22.5 ng/dl ± SD = 11.6 vs. 15.2 ± 4.5, p < 0.001), higher BMI (35.8 kg/m 2 ± 9.9 vs. 29.9 ± 5.8, p < 0.001), lower potassium (3.9 mmol/L ± 0.5 vs. 4.1 ± 0.6, p = 0.03), and more intense antihypertensive drug therapy (defined by the World Health Organization defined daily dose [6.1 ± 3.2 vs. 4.4 ± 3.0, p = 0.01]) than hypertensive patients without PA. The optimal classification tree model performed relatively poorly at differentiating those with PA from those without PA (sensitivity = 0.76, specificity = 0.86, positive predictive value = 0.87, and negative predictive value = 0.73). However, the model did reveal a subset of individuals who consistently tested negative for PA. Out of 14 patients with serum aldosterone concentration < 25.5, serum potassium > 3.55, and BMI < 27, none had PA. Conclusion: We identified a set of readily available clinical variables for identifying hypertensive patients who screened positive for PA but in whom PA was subsequently proven to be absent. Applying these criteria to our screen-positive hypertensive cohort reduces confirmatory testing by approximately 15%. Study in a larger sample size and external validation of this model is needed prior to recommending it for use in clinical decision-making.

An automated OpenMP mutation testing framework for performance optimization

Performance optimization continues to be a challenge in modern HPC software. Existing performance optimization techniques, including profiling-based and auto-tuning techniques, fail to indicate program modifications at the source level thus preventing their portability across compilers. This paper describes Muppet, a new approach that identifies program modifications called mutations aimed at improving program performance. Muppet’s mutations help developers reason about performance defects and missed opportunities to improve performance at the source code level. In contrast to compiler techniques that optimize code at intermediate representations (IR), Muppet uses the idea of source-level mutation testing to relax correctness constraints and automatically discover optimization opportunities that otherwise are not feasible using the IR. We demonstrate the Muppet’s concept in the OpenMP programming model. Muppet generates a list of OpenMP mutations that alter the program parallelism in various ways, and is capable of running a variety of optimization algorithms such as delta debugging, Bayesian Optimization and decision tree optimization to find a subset of mutations which, when applied to the original program, cause the most speedup while maintaining program correctness. When Muppet is evaluated against a diverse set of benchmark programs and proxy applications, it is capable of finding sets of mutations that induce speedup in 75.9% of the evaluated programs.

Estimating optimal decision trees for treatment assignment: The case of K > 2 treatment alternatives.

For many problems in clinical practice, multiple treatment alternatives are available. Given data from a randomized controlled trial or an observational study, an important challenge is to estimate an optimal decision rule that specifies for each client the most effective treatment alternative, given his or her pattern of pretreatment characteristics. In the present paper we will look for such a rule within the insightful family of classification trees. Unfortunately, however, there is dearth of readily accessible software tools for optimal decision tree estimation in the case of more than two treatment alternatives. Moreover, this primary tree estimation problem is also cursed with two secondary problems: a structural missingness in typical studies on treatment evaluation (because every individual is assigned to a single treatment alternative only), and a major issue of replicability. In this paper we propose solutions for both the primary and the secondary problems at stake. We evaluate the proposed solution in a simulation study, and illustrate with an application on the search for an optimal tree-based treatment regime in a randomized controlled trial on K = 3 different types of aftercare for younger women with early-stage breast cancer. We conclude by arguing that the proposed solutions may have relevance for several other classification problems inside and outside the domain of optimal treatment assignment.

Financial distress prediction using an improved particle swarm optimization wrapper feature selection method and tree boosting ensemble

Financial distress prediction (FDP) is a complex task involving both feature selection and model construction. While many studies have addressed these challenges individually, there is a lack of FDP models that integrate feature selection into the overall model building process. To address the issues of fast convergence and local optimization in particle swarm optimization (PSO), this study proposes a modified PSO algorithm with three improvement strategies. This improved PSO, known as IPSO, is embedded within state-of-the-art tree boosting ensemble models for feature selection. IPSO continuously evolves toward the optimal feature subset, preventing premature convergence and avoiding local optima. To construct the FDP model, four state-of-the-art tree boosting models are combined using an improved majority voting ensemble strategy. The integration of IPSO enhances the prediction performance of the model. Comparative experiments are conducted on samples of Chinese listed companies under short-term and long-term prediction scenarios to evaluate the proposed model. The results demonstrate that IPSO significantly improves the prediction performance, and the ensemble strategy enhances the robustness of the predictions.

Optimal tree tensor network operators for tensor network simulations: Applications to open quantum systems.

Tree tensor network states (TTNS) decompose the system wavefunction to the product of low-rank tensors based on the tree topology, serving as the foundation of the multi-layer multi-configuration time-dependent Hartree method. In this work, we present an algorithm that automatically constructs the optimal and exact tree tensor network operators (TTNO) for any sum-of-product symbolic quantum operator. The construction is based on the minimum vertex cover of a bipartite graph. With the optimal TTNO, we simulate open quantum systems, such as spin relaxation dynamics in the spin-boson model and charge transport in molecular junctions. In these simulations, the environment is treated as discrete modes and its wavefunction is evolved on equal footing with the system. We employ the Cole-Davidson spectral density to model the glassy phonon environment and incorporate temperature effects via thermo-field dynamics. Our results show that the computational cost scales linearly with the number of discretized modes, demonstrating the efficiency of our approach.

Interpolation-split: a data-centric deep learning approach with big interpolated data to boost airway segmentation performance

The morphology and distribution of airway tree abnormalities enable diagnosis and disease characterisation across a variety of chronic respiratory conditions. In this regard, airway segmentation plays a critical role in the production of the outline of the entire airway tree to enable estimation of disease extent and severity. Furthermore, the segmentation of a complete airway tree is challenging as the intensity, scale/size and shape of airway segments and their walls change across generations. The existing classical techniques either provide an undersegmented or oversegmented airway tree, and manual intervention is required for optimal airway tree segmentation. The recent development of deep learning methods provides a fully automatic way of segmenting airway trees; however, these methods usually require high GPU memory usage and are difficult to implement in low computational resource environments. Therefore, in this study, we propose a data-centric deep learning technique with big interpolated data, Interpolation-Split, to boost the segmentation performance of the airway tree. The proposed technique utilises interpolation and image split to improve data usefulness and quality. Then, an ensemble learning strategy is implemented to aggregate the segmented airway segments at different scales. In terms of average segmentation performance (dice similarity coefficient, DSC), our method (A) achieves 90.55%, 89.52%, and 85.80%; (B) outperforms the baseline models by 2.89%, 3.86%, and 3.87% on average; and (C) produces maximum segmentation performance gain by 14.11%, 9.28%, and 12.70% for individual cases when (1) nnU-Net with instant normalisation and leaky ReLU; (2) nnU-Net with batch normalisation and ReLU; and (3) modified dilated U-Net are used respectively. Our proposed method outperformed the state-of-the-art airway segmentation approaches. Furthermore, our proposed technique has low RAM and GPU memory usage, and it is GPU memory-efficient and highly flexible, enabling it to be deployed on any 2D deep learning model.

Strong Optimal Classification Trees

Decision trees are among the most interpretable and popular machine learning models that are used routinely in applications ranging from revenue management to medicine. Traditional heuristic methods, although fast, lack modeling flexibility for incorporating constraints such as fairness and do not guarantee optimality. Recent efforts aim to overcome these limitations using mixed-integer optimization (MIO) for better modeling flexibility and optimality, but speed remains an issue. In “Strong Optimal Classification Trees,” Aghaei, Gómez, and Vayanos use integer optimization and polyhedral theory to create an MIO-based formulation with a strong LO relaxation resulting in a 29% speed-up in training time compared with state-of-the-art MIO-based formulations, as well as up to an 8% improvement in out-of-sample accuracy.

Optimization and characterization of essential oil-loaded nanoemulsions for enhanced antiviral activity against tobacco mosaic virus (TMV) in tobacco plants

Tobacco mosaic virus (TMV) is a significant viral pathogen that infects various economically important crops, including tobacco, tomatoes, and cucumbers. The current study aimed to develop and optimize essential oil-loaded nanoemulsions using Response Surface Methodology (RSM) to enhance antiviral activity against TMV in Nicotiana tabacum plants. Essential oils from tea tree (Melaleuca alternifolia) and lime peel (Citrus latifolia) were chemically analyzed using gas chromatography-mass spectrometry (GC-MS). Terpinene-4-ol (70.92 %) and trans-isolimonene (33.82 %) were identified as the major components in tea tree and lime peel oils, respectively. RSM was used to optimize the nanoemulsion formulations based on oil concentration, hydrophilic-lipophilic balance (HLB), and stirring speed. Optimal tea tree oil (TTEO) and lime peel oil (LPEO) nanoemulsions were developed and characterized using Fourier-transform infrared (FTIR) spectroscopy, scanning electron microscopy (SEM), and particle size analysis. The antiviral efficacy of the optimized formulations was tested against TMV using RT-qPCR analysis and physiological measurements. TTEO nanoemulsions significantly inhibited TMV expression by 89.78 %, while LPEO nanoemulsions achieved a 42.22 % reduction after six days. Additionally, these essential oils (EOs) enhanced plant defense mechanisms by modulating the activities of phenylalanine ammonia-lyase (PAL) and peroxidase (POD), along with maintaining chlorophyll levels. This study demonstrates that TTEO and LPEO nanoemulsions offer promising eco-friendly antiviral agents for TMV management in tobacco plants. The research underscores the potential of essential oil-based formulations in mitigating viral infections in crops, providing a sustainable alternative to synthetic chemicals.

Interpretable artificial intelligence to optimise use of imatinib after resection in patients with localised gastrointestinal stromal tumours: an observational cohort study

Current guidelines recommend use of adjuvant imatinib therapy for many patients with gastrointestinal stromal tumours (GISTs); however, its optimal treatment duration is unknown and some patient groups do not benefit from the therapy. We aimed to apply state-of-the-art, interpretable artificial intelligence (ie, predictions or prescription logic that can be easily understood) methods on real-world data to establish which groups of patients with GISTs should receive adjuvant imatinib, its optimal treatment duration, and the benefits conferred by this therapy. In this observational cohort study, we considered for inclusion all patients who underwent resection of primary, non-metastatic GISTs at the Memorial Sloan Kettering Cancer Center (MSKCC; New York, NY, USA) between Oct 1, 1982, and Dec 31, 2017, and who were classified as intermediate or high risk according to the Armed Forces Institute of Pathology Miettinen criteria and had complete follow-up data with no missing entries. A counterfactual random forest model, which used predictors of recurrence (mitotic count, tumour size, and tumour site) and imatinib duration to infer the probability of recurrence at 7 years for a given patient under each duration of imatinib treatment, was trained in the MSKCC cohort. Optimal policy trees (OPTs), a state-of-the-art interpretable AI-based method, were used to read the counterfactual random forest model by training a decision tree with the counterfactual predictions. The OPT recommendations were externally validated in two cohorts of patients from Poland (the Polish Clinical GIST Registry), who underwent GIST resection between Dec 1, 1981, and Dec 31, 2011, and from Spain (the Spanish Group for Research in Sarcomas), who underwent resection between Oct 1, 1987, and Jan 30, 2011. Among 1007 patients who underwent GIST surgery in MSKCC, 117 were included in the internal cohort; for the external cohorts, the Polish cohort comprised 363 patients and the Spanish cohort comprised 239 patients. The OPT did not recommend imatinib for patients with GISTs of gastric origin measuring less than 15·9 cm with a mitotic count of less than 11·5 mitoses per 5 mm2 or for those with small GISTs (<5·4 cm) of any site with a count of less than 11·5 mitoses per 5 mm2. In this cohort, the OPT cutoffs had a sensitivity of 92·7% (95% CI 82·4-98·0) and a specificity of 33·9% (22·3-47·0). The application of these cutoffs in the two external cohorts would have spared 38 (29%) of 131 patients in the Spanish cohort and 44 (35%) of 126 patients in the Polish cohort from unnecessary treatment with imatinib. Meanwhile, the risk of undertreating patients in these cohorts was minimal (sensitivity 95·4% [95% CI 89·5-98·5] in the Spanish cohort and 92·4% [88·3-95·4] in the Polish cohort). The OPT tested 33 different durations of imatinib treatment (<5 years) and found that 5 years of treatment conferred the most benefit. If the identified patient subgroups were applied in clinical practice, as many as a third of the current cohort of candidates who do not benefit from adjuvant imatinib would be encouraged to not receive imatinib, subsequently avoiding unnecessary toxicity on patients and financial strain on health-care systems. Our finding that 5 years is the optimal duration of imatinib treatment could be the best source of evidence to inform clinical practice until 2028, when a randomised controlled trial with the same aims is expected to report its findings. National Cancer Institute.

Piping network optimization for district heating system using an enhanced Genetic Algorithm searching method

Given the substantial construction and operational expenses associated with a district heating system (DHS), achieving an optimal layout for the piping network is paramount for its successful deployment. In this study, the optimization of DHS piping configuration has been explored. Traditional exhaustive search methods for network design are often impractical due to computational constraints, making Genetic Algorithm (GA) a preferred alternative for navigating the vast search space of optimization problems efficiently. However, GA, which relies on probabilistic heuristics, may not always pinpoints the most effective solutions, particularly those in close proximity to the current near-optimal configuration. To address this issue, an enhanced GA-based neighboring search method for identifying optimal or near-optimal piping layout for DHS more effectively has been developed in this study. When a local minimum is detected in the GA optimization process, the method initiates a neighboring search by selecting an elite candidate. The link with the highest piping cost from the elite candidate's configuration is identified. Subsequently, one of the other nodes in the configuration is connected to the nodes of the identified link to explore solutions beyond the local optimum. This new approach was firstly validated against an Optimal Communication Spanning Tree (OCST) benchmark problem, where it demonstrated superior efficacy by achieving higher success rate and quicker first-hit generation compared to conventional GA method. Specifically, this method showed a 60 % success rate with a minimum first-hit generation number of 140, outperforming the traditional GA's 40 % success rate and 263 generations. Further modification to the OCST benchmark to better simulate a real-world DHS application underscored the ability of this neighboring search method to exceed the previously established optimal configuration, uncovering a “better' solution with superior fitness value. This promising methodology was subsequently applied to the hypothetical design of a DHS piping network, illustrating its potential to enhance the planning and implementation of efficient, cost-effective district heating systems.

Finding Optimal Spanning Trees For Damaged Networks

We use a representation for the spanning tree where a parent function maps non-root vertices to vertices. Two spanning trees are defined to be adjacent if their function representations differ at exactly one vertex. Given a graph G , we show that the graph H with all spanning trees of G as vertices and any two vertices being adjacent if and only if their parent functions differ at exactly one vertex is connected.

Phylo2Vec: a vector representation for binary trees

Abstract Binary phylogenetic trees inferred from biological data are central to understanding the shared history among evolutionary units. However, inferring the placement of latent nodes in a tree is computationally expensive. State-of-the-art methods rely on carefully designed heuristics for tree search, using different data structures for easy manipulation (e.g., classes in object-oriented programming languages) and readable representation of trees (e.g., Newick-format strings). Here, we present Phylo2Vec, a parsimonious encoding for phylogenetic trees that serves as a unified approach for both manipulating and representing phylogenetic trees. Phylo2Vec maps any binary tree with n leaves to a unique integer vector of length n − 1. The advantages of Phylo2Vec are fourfold: i) fast tree sampling, (ii) compressed tree representation compared to a Newick string, iii) quick and unambiguous verification if two binary trees are identical topologically, and iv) 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 scheme can efficiently traverse the vastness of tree space from a random to an optimal tree.