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Hilmar Lapp CV

Dir, IT
Biostatistics & Bioinformatics
Box 90090, North Building 119, Durham, NC 27708
304 Research Drive, North Building 119, Durham, NC 27708
CV

Selected Publications


Hierarchical Conditioning of Diffusion Models Using Tree-of-Life for Studying Species Evolution

Conference Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) · January 1, 2025 A central problem in biology is to understand how organisms evolve and adapt to their environment by acquiring variations in the observable characteristics or traits of species across the tree of life. With the growing availability of large-scale image rep ... Full text Cite

A FAIR and modular image-based workflow for knowledge discovery in the emerging field of imageomics

Journal Article Methods in Ecology and Evolution · June 1, 2024 Image-based machine learning tools are an ascendant ‘big data’ research avenue. Citizen science platforms, like iNaturalist, and museum-led initiatives provide researchers with an abundance of data and knowledge to extract. These include extraction of meta ... Full text Cite

Meeting Report for the Phenoscape TraitFest 2023 with Comments on Organising Interdisciplinary Meetings

Journal Article Biodiversity Information Science and Standards · March 6, 2024 The Phenoscape project has developed ontology-based tools and a knowledge base that enables the integration and discovery of phenotypes across species from the scientific literature. The Phenoscape TraitFest 2023 event aimed to promote innovative a ... Full text Cite

rphenoscate: An R package for semantics-aware evolutionary analyses of anatomical traits

Journal Article Methods in Ecology and Evolution · October 1, 2023 Organismal anatomy is a hierarchical system of anatomical entities often imposing dependencies among multiple morphological characters. Ontologies provide a formal and computable framework for incorporating prior biological knowledge about anatomical depen ... Full text Cite

Discovering Novel Biological Traits from Images Using Phylogeny-Guided Neural Networks

Conference Proceedings of the ACM SIGKDD International Conference on Knowledge Discovery and Data Mining · August 6, 2023 Discovering evolutionary traits that are heritable across species on the tree of life (also referred to as a phylogenetic tree) is of great interest to biologists to understand how organisms diversify and evolve. However, the measurement of traits is often ... Full text Cite

Assessing Bayesian Phylogenetic Information Content of Morphological Data Using Knowledge From Anatomy Ontologies.

Journal Article Systematic biology · October 2022 Morphology remains a primary source of phylogenetic information for many groups of organisms, and the only one for most fossil taxa. Organismal anatomy is not a collection of randomly assembled and independent "parts", but instead a set of dependent and hi ... Full text Open Access Cite

Phyloreferences: Tree-Native, Reproducible, and Machine-Interpretable Taxon Concepts

Journal Article Philosophy, Theory, and Practice in Biology · January 27, 2022 Evolutionary and organismal biology have become inundated with data. At the same rate, we are experiencing a surge in broader evolutionary and ecological syntheses for which tree-thinking is the staple for a variety of post-tree analyses. To fully ... Full text Cite

A new phylogenetic data standard for computable clade definitions: the Phyloreference Exchange Format (Phyx).

Journal Article PeerJ · January 2022 To be computationally reproducible and efficient, integration of disparate data depends on shared entities whose matching meaning (semantics) can be computationally assessed. For biodiversity data one of the most prevalent shared entities for linking data ... Full text Open Access Cite

JPhyloRef: a tool for testing and resolving phyloreferences

Journal Article Journal of Open Source Software · August 14, 2021 Full text Cite

Seed Patterns for Modeling Trees

Conference Studies in Health Technology and Informatics · May 7, 2021 Trees - i.e., the type of data structure known under this name - are central to many aspects of knowledge organization.We investigate some central design choices concerning the ontological modeling of such trees. In particular, we consider the limits of wh ... Full text Cite

Enabling Machines to Integrate Biodiversity Data with Evolutionary Knowledge

Journal Article Biodiversity Information Science and Standards · October 2, 2020 Most biological data and knowledge are directly or indirectly linked to biological taxa via taxon names. Using taxon names is one of the most fundamental and ubiquitous ways in which a wide range of biological data are integrated, aggregated, and i ... Full text Cite

A Logical Model of Homology for Comparative Biology.

Journal Article Systematic biology · March 2020 There is a growing body of research on the evolution of anatomy in a wide variety of organisms. Discoveries in this field could be greatly accelerated by computational methods and resources that enable these findings to be compared across different studies ... Full text Open Access Cite

Application programming interfaces for knowledge transfer and generation in the life sciences and healthcare.

Journal Article NPJ Digit Med · 2020 Storing very large amounts of data and delivering them to researchers in an efficient, verifiable, and compliant manner, is one of the major challenges faced by health care providers and researchers in the life sciences. The electronic health record (EHR) ... Full text Open Access Link to item Cite