Tree-based Representation Research Articles

A Cohort Tree-based Representation and a Multimorbidity Progression Across Pregnancies in Scotland

Pregnancy-related research using routinely collected data is increasing. Electronic Health Records (EHR) are a robust resource because they can provide information on a large population of pregnant women covering prolonged periods at a reasonable cost. Moreover, information is collected prospectively and is thus free from recall bias. However, these data sources also present challenges. Information is gathered for clinical purposes and often recorded in different datasets (prescriptions, hospital admission, demography, birth records, etc.). Therefore, a significant data management effort must be made to convert all the information into structured and meaningful datasets in which identifying the timing of conception, outcomes of interest, multiple pregnancies, and interpregnancy periods can easily be done. In this study, we linked Scottish Maternity Records between 2007 and 2021 (1,575,153 pregnancies, 493,629 women) to demographics data, datasets with International Classification of Diseases (ICD) diagnostic codes for all inpatient stays and day cases in hospitals, and Prescribing Information System (PIS) for data on all medications from primary care. After combining these datasets using R codes, we developed a simple tree-based algorithm that visually represents each woman at each pregnancy and the related health conditions. Presenting data in this way helps identify relevant clinical questions and the temporal relation of different pregnancies. As an example, we identified the progression of multimorbidity through pregnancies and characterised how multimorbidity changes from one pregnancy to another, considering the woman's health conditions and social class.

Imperative Genetic Programming

Genetic programming (GP) has a long-standing tradition in the evolution of computer programs, predominantly utilizing tree and linear paradigms, each with distinct advantages and limitations. Despite the rapid growth of the GP field, there have been disproportionately few attempts to evolve ’real’ Turing-like imperative programs (as contrasted with functional programming) from the ground up. Existing research focuses mainly on specific special cases where the structure of the solution is partly known. This paper explores the potential of integrating tree and linear GP paradigms to develop an encoding scheme that universally supports genetic operators without constraints and consistently generates syntactically correct Python programs from scratch. By blending the symmetrical structure of tree-based representations with the inherent asymmetry of linear sequences, we created a versatile environment for program evolution. Our approach was rigorously tested on 35 problems characterized by varying Halstead complexity metrics, to delineate the approach’s boundaries. While expected brute-force program solutions were observed, our method yielded more sophisticated strategies, such as optimizing a program by restricting the division trials to the values up to the square root of the number when counting its proper divisors. Despite the recent groundbreaking advancements in large language models, we assert that the GP field warrants continued research. GP embodies a fundamentally different computational paradigm, crucial for advancing our understanding of natural evolutionary processes.

A Global and Local Surrogate-Assisted Genetic Programming Approach to Image Classification

Genetic programming (GP) has achieved promising performance in image classification. However, GP-based methods usually require a long computation time for fitness evaluations, posing a challenge to real-world applications. Surrogate models can be efficiently computable approximations of expensive fitness evaluations. However, most existing surrogate methods are designed for evolutionary computation techniques with a vector-based representation consisting of numerical values, thus cannot be directly used for GP with a tree-based representation consisting of functions/operators. The variable sizes of GP trees further increase the difficulty of building the surrogate model for fitness approximations. To address these limitations, we propose a new surrogate-assisted GP approach including global and local surrogate models, which can accelerate the evolutionary learning process and achieve competitive classification performance simultaneously. The global surrogate model can assist GP in exploring the entire search space, while the local surrogate model can speed up convergence and further improve performance. Furthermore, a new surrogate training set is constructed to assist in establishing the relationship between the GP tree and its fitness, and effective surrogate models can be built accordingly. Experimental results on ten datasets of varying difficulty show that the new approach significantly reduces the computational cost of the GP-based method without sacrificing the classification accuracy. The comparisons with other state-of-the-art methods also demonstrate the effectiveness of the new approach. Further analysis reveals the significance of the global and local surrogates and the new surrogate training set on improving or maintaining the performance of the proposed approach while reducing the computational cost.

Predicting Task Planning Ability for Learners Engaged in Searching as Learning Based on Tree-Structured Long Short-Term Memory Networks

The growing utilization of web-based search engines for learning purposes has led to increased studies on searching as learning (SAL). In order to achieve the desired learning outcomes, web learners have to carefully plan their learning objectives. Previous SAL research has proposed the significant influence of task planning quality on learning outcomes. Therefore, accurately predicting web-based learners’ task planning abilities, particularly in the context of SAL, is of paramount importance for both web-based search engines and recommendation systems. To solve this problem, this paper proposes a method for predicting the ability of task planning for web learners. Specifically, we first introduced a tree-based representation method to capture how learners plan their learning tasks. Subsequently, we proposed a method based on the deep learning technique to accurately predict the SAL task planning ability for web learners. Experimental results indicate that, compared to baseline approaches, our proposed method can provide a more effective representation of learners’ task planning and deliver more accurate predictions of learners’ task planning abilities in SAL.

LegalHTML: Semantic mark-up of legal acts using web technologies

We introduce here LegalHTML, an extension of the HTML language thought for representing legal acts. LegalHTML has been conceived in the context of an exploratory study conducted for the Publications Office of the European Union, with the objective of overcoming the proliferation of formats for the electronic redaction of legal acts, dedicated to different steps of the editorial process (e.g. first draft, content editing, proof reading, introducing semantics, publishing) and of realizing a model and a language that could bind all processes and exigencies under a common umbrella. LegalHTML satisfies these requirements by providing an explicit domain language addressing all structural aspects of an act, such as articles, paragraphs, items, references and an associated ontology (foreseeing both inline annotations through RDFa and explicit RDF code within script elements) providing rich semantics to describe the editorial and jurisdictional history of the act and to insert references to entities of the domain. Being based on HTML, presentation is also offered by the same language, an aspect missing from all most notable standards for the legal domain. Furthermore, LegalHTML addresses consolidation of an act and its subsequent modifications into a single document using a tree-based representation of the original content and of its modified versions. Finally, alongside the language & ontology, we implemented a CSS stylesheet for the default rendering of LegalHTML documents and a JavaScript file imbuing documents with an API supporting TOC generation, footnote cross-references and the said point-in-time visualization of consolidated legal acts.

Behavior Trees and State Machines in Robotics Applications

Autonomous robots combine skills to form increasingly complex behaviors, called missions. While skills are often programmed at a relatively low abstraction level, their coordination is architecturally separated and often expressed in higher-level languages or frameworks. State machines have been the go-to language to model behavior for decades, but recently, behavior trees have gained attention among roboticists. Originally designed to model autonomous actors in computer games, behavior trees offer an extensible tree-based representation of missions and are claimed to support modular design and code reuse. Although several implementations of behavior trees are in use, little is known about their usage and scope in the real world. How do concepts offered by behavior trees relate to traditional languages, such as state machines? How are concepts in behavior trees and state machines used in actual applications? This paper is a study of the key language concepts in behavior trees as realized in domain-specific languages (DSLs), internal and external DSLs offered as libraries, and their use in open-source robotic applications supported by the Robot Operating System (ROS). We analyze behavior-tree DSLs and compare them to the standard language for behavior models in robotics: state machines. We identify DSLs for both behavior-modeling languages, and we analyze five in-depth. We mine open-source repositories for robotic applications that use the analyzed DSLs and analyze their usage. We identify similarities between behavior trees and state machines in terms of language design and the concepts offered to accommodate the needs of the robotics domain. We observed that the usage of behavior-tree DSLs in open-source projects is increasing rapidly. We observed similar usage patterns at model structure and at code reuse in the behavior-tree and state-machine models within the mined open-source projects. We contribute all extracted models as a dataset, hoping to inspire the community to use and further develop behavior trees, associated tools, and analysis techniques.

A configuration-based heatbath-CI for spin-adapted multireference electronic structure calculations with large active spaces.

This work reports on a spin-pure configuration-based implementation of the heatbath configuration interaction (HCI) algorithm for selective configuration interaction. Besides the obvious advantage of being spin-pure, the presented method combines the compactness of the configurational ansatz with the known efficiency of the HCI algorithm and a variety of algorithmic and conceptual ideas to achieve a high level of performance. In particular, through pruning of the selected configurational space after HCI selection by means of a more strict criterion, a more compact wavefunction representation is obtained. Moreover, the underlying logic of the method allows us to minimize the number of redundant matrix-matrix multiplications while making use of just-in-time compilation to achieve fast diagonalization of the Hamiltonian. The critical search for 2-electron connections within the configurational space is facilitated by a tree-based representation thereof as suggested previously by Gopal et al. Usage of a prefix-based parallelization and batching during the calculation of the PT2-correction leads to a good load balancing and significantly reduced memory requirements for these critical steps of the calculation. In this way, the need for a semistochastic approach to the PT2 correction is avoided even for large configurational spaces. Finally, several test-cases are discussed to demonstrate the strengths and weaknesses of the presented method.

Unbiased pangenome graphs.

Pangenome variation graphs model the mutual alignment of collections of DNA sequences. A set of pairwise alignments implies a variation graph, but there are no scalable methods to generate such a graph from these alignments. Existing related approaches depend on a single reference, a specific ordering of genomes or a de Bruijn model based on a fixed k-mer length. A scalable, self-contained method to build pangenome graphs without such limitations would be a key step in pangenome construction and manipulation pipelines. We design the seqwish algorithm, which builds a variation graph from a set of sequences and alignments between them. We first transform the alignment set into an implicit interval tree. To build up the variation graph, we query this tree-based representation of the alignments to reduce transitive matches into single DNA segments in a sequence graph. By recording the mapping from input sequence to output graph, we can trace the original paths through this graph, yielding a pangenome variation graph. We present an implementation that operates in external memory, using disk-backed data structures and lock-free parallel methods to drive the core graph induction step. We demonstrate that our method scales to very large graph induction problems by applying it to build pangenome graphs for several species. seqwish is published as free software under the MIT open source license. Source code and documentation are available at https://github.com/ekg/seqwish. seqwish can be installed via Bioconda https://bioconda.github.io/recipes/seqwish/README.html or GNU Guix https://github.com/ekg/guix-genomics/blob/master/seqwish.scm.

Imaging-based representation and stratification of intra-tumor heterogeneity via tree-edit distance

Personalized medicine is the future of medical practice. In oncology, tumor heterogeneity assessment represents a pivotal step for effective treatment planning and prognosis prediction. Despite new procedures for DNA sequencing and analysis, non-invasive methods for tumor characterization are needed to impact on daily routine. On purpose, imaging texture analysis is rapidly scaling, holding the promise to surrogate histopathological assessment of tumor lesions. In this work, we propose a tree-based representation strategy for describing intra-tumor heterogeneity of patients affected by metastatic cancer. We leverage radiomics information extracted from PET/CT imaging and we provide an exhaustive and easily readable summary of the disease spreading. We exploit this novel patient representation to perform cancer subtyping according to hierarchical clustering technique. To this purpose, a new heterogeneity-based distance between trees is defined and applied to a case study of prostate cancer. Clusters interpretation is explored in terms of concordance with severity status, tumor burden and biological characteristics. Results are promising, as the proposed method outperforms current literature approaches. Ultimately, the proposed method draws a general analysis framework that would allow to extract knowledge from daily acquired imaging data of patients and provide insights for effective treatment planning.

ASTENS-BWA: Searching partial syntactic similar regions between source code fragments via AST-based encoded sequence alignment

Code search is a common activity in software development, and code-to-code search can benefit in a wide range of use-case scenarios. Code-to-code search uses a code fragment as the query for searching similar code fragments from large corpora. The results of a search can be applied to some software engineering tasks, such as search-based code recommendation, data-driven program repairing, and software plagiarism detection. To be put into daily use, the code-to-code search needs to find similar code fragments accurately and efficiently in a large dataset. Some search engines can locate exactly similar code, but are not able to search syntactical clones. Therefore, we propose ASTENS-BWA, a novel approach for searching syntactic similar code regions between code fragments via a tree-based sequence alignment. Source code has been transformed into a tree-based sequence that contains the structure information, and a sequence alignment algorithm has been applied to find similar regions. We evaluate ASTENS-BWA on three different tasks, the results demonstrate that our approach can find syntactical similar regions for programming code and retrieve similar code fragments fast and with high accuracy. As a code clone detection tool, ASTENS-BWA can report clone pairs in a high recall, but it needs manually check to reduce the false alarms. ASTENS-BWA is scalable and can report cloned code fragments in seconds for a code corpus of million lines of code. • Novel code clone search approach that scales to large source code repositories. • Quick searching syntactical clones between code fragments via tree-based representation. • Code clone search approach that can outperform state-of-the-art techniques. • Application of the proposed approach towards code recommendation and clone detection.

A novel tree-based representation for evolving analog circuits and its application to memristor-based pulse generation circuit

When applying evolutionary algorithms to circuit design automation, circuit representation is the first consideration. There have been several studies applying different circuit representations. However, they still have some problems, such as lack of design ability, which means the diversity of evolved circuits was limited by the circuit representation, and inefficient transformation from circuit representation into SPICE (Simulation Program with Integrated Circuit Emphasis) netlist. In this paper, a novel tree-based circuit representation for analog circuits is proposed, which is equipped with an intuitive and three-terminal devices friendly mapping rule between circuit representation and SPICE netlist, as well as a suitable crossover operator. Based on the proposed representation, a framework for automated analog circuit design using genetic programming is proposed to evolve both the circuit topology and device values. Three benchmark circuits are applied to evaluate the proposed approach, showing that the proposed method is feasible and evolves analog circuits with better fitness and number of components while using less fitness evaluations than existing approaches. Furthermore, considering physical scalability limits of conventional circuit elements and the increased interest in emerging technologies, a memristor-based pulse generation circuit is also evolved based on the proposed method. The feasibility of the evolved circuits is verified by circuit simulation successfully. The experiment results show that the evolved memristive circuit is more compact and has better energy efficiency compared with existing manually-designed circuits.

Model and system for scientific workflows represented in file system directory tree

In this paper, we present a new workflow representation model which is based on directory trees. We show the implementation of the model inside the EPISODES Platform — a portal for analyses related to anthropogenic hazards. Most workflow management systems use a DAG or custom programming language to encode a workflow. While this works well in many cases, we believe that there is a class of applications for which our approach is a better fit.This paper demonstrates how workflows can be efficiently represented in a file system tree. In our model, each workflow step is encoded as a directory. This enables natural encapsulation and modularity of the data alongside the workflow structure. We show how fundamental patterns such as sequence, merge, fork, and cycle are encoded. We believe that the presented directory tree-based representation is well suited for workflow systems that emphasize interactive composition processes. By implementing a rich GUI with built-in data visualization tools it may be particularly useful for exploratory programming where interactivity, dynamicity, and extensibility are crucial. The solution supports multi-level workflow nesting, reuse, sharing, and live collaboration in the workflow design process. The integrated workflow execution engine is scalable and supports automatic execution on high-performance distributed infrastructure. Our model was implemented and evaluated within the EPISODES Platform (Orlecka-Sikora et al., 2020), a workflow management system used by over 1400 users interested in research into anthropogenic hazards.

Efficient and compact representations of some non-canonical prefix-free codes

For many kinds of prefix-free codes there are efficient and compact alternatives to the traditional tree-based representation. Since these put the codes into canonical form, however, they can only be used when we can choose the order in which codewords are assigned to symbols. In this paper we first show how, given a probability distribution over an alphabet of σ symbols, we can store an optimal alphabetic prefix-free code in O(σlg⁡L) bits such that we can encode and decode any codeword of length ℓ in O(min⁡(ℓ,lg⁡L)) time, where L is the maximum codeword length. With O(2Lϵ) further bits, for any constant ϵ>0, we can encode and decode O(lg⁡ℓ) time. We then show how to store a nearly optimal alphabetic prefix-free code in o(σ) bits such that we can encode and decode in constant time. We also consider a kind of optimal prefix-free code introduced recently where the codewords' lengths are non-decreasing if arranged in lexicographic order of their reverses. We reduce their storage space to O(σlg⁡L) while maintaining encoding and decoding times in O(ℓ). We also show how, with O(2ϵL) further bits, we can encode and decode in constant time. All of our results hold in the word-RAM model.

Analysis of co-occurring and mutually exclusive amino acid changes and detection of convergent and divergent evolution events in SARS-CoV-2

The inflation of SARS-CoV-2 lineages with a high number of accumulated mutations (such as the recent case of Omicron) has risen concerns about the evolutionary capacity of this virus. Here, we propose a computational study to examine non-synonymous mutations gathered within genomes of SARS-CoV-2 from the beginning of the pandemic until February 2022. We provide both qualitative and quantitative descriptions of such corpus, focusing on statistically significant co-occurring and mutually exclusive mutations within single genomes. Then, we examine in depth the distributions of mutations over defined lineages and compare those of frequently co-occurring mutation pairs. Based on this comparison, we study mutations’ convergence/divergence on the phylogenetic tree. As a result, we identify 1,818 co-occurring pairs of non-synonymous mutations showing at least one event of convergent evolution and 6,625 co-occurring pairs with at least one event of divergent evolution. Notable examples of both types are shown by means of a tree-based representation of lineages, visually capturing mutations’ behaviors. Our method confirms several well-known cases; moreover, the provided evidence suggests that our workflow can explain aspects of the future mutational evolution of SARS-CoV-2.

OLOGRAM-MODL: mining enriched n-wise combinations of genomic features with Monte Carlo and dictionary learning.

Most epigenetic marks, such as Transcriptional Regulators or histone marks, are biological objects known to work together in n-wise complexes. A suitable way to infer such functional associations between them is to study the overlaps of the corresponding genomic regions. However, the problem of the statistical significance of n-wise overlaps of genomic features is seldom tackled, which prevent rigorous studies of n-wise interactions. We introduce OLOGRAM-MODL, which considers overlaps between n ≥ 2 sets of genomic regions, and computes their statistical mutual enrichment by Monte Carlo fitting of a Negative Binomial distribution, resulting in more resolutive P-values. An optional machine learning method is proposed to find complexes of interest, using a new itemset mining algorithm based on dictionary learning which is resistant to noise inherent to biological assays. The overall approach is implemented through an easy-to-use CLI interface for workflow integration, and a visual tree-based representation of the results suited for explicability. The viability of the method is experimentally studied using both artificial and biological data. This approach is accessible through the command line interface of the pygtftk toolkit, available on Bioconda and from https://github.com/dputhier/pygtftk

Cross-lingual transfer learning for relation extraction using Universal Dependencies

This paper focuses on the task of cross-language relation extraction, which aims to identify the semantic relations holding between entities in the text. The goal of the task is to train classifiers for low-resource languages by means of the annotated data from high-resource languages. Related methods usually employ parallel data or Machine Translator (MT) to project annotated data from a source to a target language. However, the availability and the quality of parallel data and MT are big challenges for low-resource languages. In this paper, a novel transfer learning method is presented for this task. The key idea is to utilize a tree-based representation of data, which is highly informative for classifying semantic relations, and also shared among different languages. All the training and test data are shown using this representation. We propose to use the Universal Dependency (UD) parsing, which is a language-agnostic formalism for representation of syntactic structures. Equipping UD parse trees with multi-lingual word embeddings makes an ideal representation for the cross-language relation extraction task. We propose two deep networks to use this representation. The first one utilizes the Shortest Dependency Path of UD trees, while the second employs the UD-based positional embeddings. Experiments are performed using SemEval 2010-task 8 training data, whereas French and Farsi are the test languages. The results show 63.9% and 56.2% F1 scores, for French and Farsi test data, respectively, which are 14.4% and 17.9% higher than the baseline. This work can be considered a simple yet powerful baseline for further investigation into the cross-language tasks.

BROCELIANDE: A COMPARATIVE STUDY OF ATTRIBUTE PROFILES AND FEATURE PROFILES FROM DIFFERENT ATTRIBUTES

Abstract. Morphological attribute profiles (APs) are among the most effective spatial-spectral methods to perform multilevel image description based on hierarchical tree-based representation. They have been widely applied to the processing and characterization of remote sensing images, in particular to tackle classification task, in the literature. Recently, a novel extension of APs called FPs has been proposed by replacing pixel gray-levels with some statistical and geometrical features when forming the output profiles. FPs have been proved to be more efficient than the standard APs when generated from both inclusion and partition trees. The motivation of this article is to conduct a comparative study of APs and FPs using different attributes including some novel ones that have not been used in the literature. We also present our developed library called Broceliande, which proposes efficient implementation of APs and FPs to perform remote sensing image classification, with various choices of tree structures as well as attributes. We perform our experiments on two high resolution optical image data sets and provide comparative results of APs and FPs, showing and confirming their effectiveness to describe and classify remote sensing images.

Destructiveness of lexicographic parsimony pressure and alleviation by a concatenation crossover in genetic programming

For theoretical analyses there are two specifics distinguishing GP from many other areas of evolutionary computation: the variable size representations, in particular yielding a possible bloat (i.e. the growth of individuals with redundant parts); and also the role and the realization of crossover, which is particularly central in GP due to the tree-based representation. Whereas some theoretical work on GP has studied the effects of bloat, crossover had surprisingly little share in this work.We analyze a simple crossover operator in combination with randomized local search, where a preference for small solutions minimizes bloat (lexicographic parsimony pressure); we denote the resulting algorithm Concatenation Crossover GP. We consider three variants of the well-studied Majority test function, adding large plateaus in different ways to the fitness landscape and thus giving a test bed for analyzing the interplay of variation operators and bloat control mechanisms in a setting with local optima. We show that the Concatenation Crossover GP can efficiently optimize these test functions, while local search cannot be efficient for all three variants independent of employing bloat control.

Component trees for image sequences and streams

Morphological hierarchies now form a well-established framework for (still) image modeling and processing. However, their extension to time-related data remains largely unexplored. In this paper, we address such a topic and show how to analyze image sequences with tree-based representations. To do so, we distinguish between three kinds of models, namely spatial, temporal and spatial-temporal hierarchies. For each of them, we review different strategies to build the hierarchy from an image sequence. We also propose some algorithms to update such trees when new images are appended to the series and we compared the time complexity with tree building from scratch. We illustrate our findings with the max and min-tree structures built on grayscale data provided by Satellite Image Time Series that are gathering a growing interest in Earth Observation. Besides, we provide a comparative study for different hierarchies with classification experiments.

Probabilistic tree-based representation for solving minimum cost integer flow problems with nonlinear non-convex cost functions

The minimum cost flow problem (MCFP) is the most generic variation of the network flow problem which aims to transfer a commodity throughout the network to satisfy demands. The problem size (in terms of the number of nodes and arcs) and the shape of the cost function are the most critical factors when considering MCFPs. Existing mathematical programming techniques often assume the cost functions to be linear or convex. Unfortunately, the linearity and convexity assumptions are too restrictive for modelling many real-world scenarios. In addition, many real-world MCFPs are large-scale, with networks having a large number of nodes and arcs. In this paper, we propose a probabilistic tree-based genetic algorithm (PTbGA) for solving large-scale minimum cost integer flow problems with nonlinear non-convex cost functions. We first compare this probabilistic tree-based representation scheme with the priority-based representation scheme, which is the most commonly-used representation for solving MCFPs. We then compare the performance of PTbGA with that of the priority-based genetic algorithm (PrGA), and two state-of-the-art mathematical solvers on a set of MCFP instances. Our experimental results demonstrate the superiority and efficiency of PTbGA in dealing with large-sized MCFPs, as compared to the PrGA method and the mathematical solvers.