Hilmar Lapp

According to our database, Hilmar Lapp authored at least 47 papers between 1999 and 2025.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2025

BioCLIP 2: Emergent Properties from Scaling Hierarchical Contrastive Learning.

Jianyang Gu, Samuel Stevens, Elizabeth G. Campolongo, Matthew J. Thompson, Net Zhang, Jiaman Wu, Andrei Kopanev, Zheda Mai, Alexander E. White, James P. Balhoff, Wasila M. Dahdul, Daniel I. Rubenstein, Hilmar Lapp, Tanya Y. Berger-Wolf, Wei-Lun Chao, Yu Su

CoRR, May, 2025

Optimizing Image Capture for Computer Vision-Powered Taxonomic Identification and Trait Recognition of Biodiversity Specimens.

Alyson East, Elizabeth G. Campolongo, Luke Meyers, S. M. Rayeed, Samuel Stevens, Iuliia Zarubiieva, Isadora E. Fluck, Jennifer C. Girón, Maximiliane Jousse, Scott C. Lowe, Kayla I Perry, Isabelle Betancourt, Noah Charney, Evan Donoso, Nathan Fox, Kim J. Landsbergen, Ekaterina Nepovinnykh, Michelle Ramirez, Parkash Singh, Khum Thapa-Magar, Matthew J. Thompson, Evan Waite, Tanya Y. Berger-Wolf, Hilmar Lapp, Paula M. Mabee, Graham Taylor, Sydne Record

CoRR, May, 2025

Building Machine Learning Challenges for Anomaly Detection in Science.

Elizabeth G. Campolongo, Yuan-Tang Chou, Ekaterina Govorkova, Wahid Bhimji, Wei-Lun Chao, Chris Harris, Shih-Chieh Hsu, Hilmar Lapp, Mark S. Neubauer, Josephine M. Namayanja, Aneesh Subramanian, Philip C. Harris, Advaith Anand, David Edward Carlyn, Subhankar Ghosh, Christopher G. Lawrence, Eric A. Moreno, Ryan Raikman, Jiaman Wu, Ziheng Zhang, Bayu Adhi, Mohammad Ahmadi Gharehtoragh, Saúl Alonso-Monsalve, Marta Babicz, Furqan Baig, Namrata Banerji, William Bardon, Tyler Barna, Tanya Y. Berger-Wolf, Adji Bousso Dieng, Micah Brachman, Quentin Buat, David C. Y. Hui, Phuong Cao, Franco Cerino, Yi-Chun Chang, Shivaji Chaulagain, An-Kai Chen, Deming Chen, Eric Chen, Chia-Jui Chou, Zih-Chen Ciou, Miles Cochran-Branson, Artur Cordeiro Oudot Choi, Michael Coughlin, Matteo Cremonesi, Maria Dadarlat, Peter Darch, Malina Desai, Daniel Diaz, Steven Dillmann, Javier Duarte, Isla Duporge, Urbas Ekka, Saba Entezari Heravi, Hao Fang, Rian Flynn, Geoffrey Fox, Emily Freed, Hang Gao, Jing Gao, Julia Gonski, Matthew J. Graham, Abolfazl Hashemi, Scott Hauck, James Hazelden, Joshua Henry Peterson, Duc Hoang, Wei Hu, Mirco Hünnefeld, David Hyde, Vandana P. Janeja, Nattapon Jaroenchai, Haoyi Jia, Yunfan Kang, Maksim Kholiavchenko, Elham E Khoda, Sangin Kim, Aditya Kumar, Bo-Cheng Lai, Trung Le, Chi-Wei Lee, JangHyeon Lee, Shaocheng Lee, Suzan van der Lee, Charles Lewis, Haitong Li, Haoyang Li, Henry Liao, Mia Liu, Xiaolin Liu, Xiulong Liu, Vladimir Loncar, Fangzheng Lyu, Ilya Makarov, Abhishikth Mallampalli Chen-Yu Mao, Alexander Michels, Alexander Migala, Farouk Mokhtar, Mathieu Morlighem

CoRR, March, 2025

Static Segmentation by Tracking: A Frustratingly Label-Efficient Approach to Fine-Grained Segmentation.

Zhenyang Feng, Zihe Wang, Saul Ibaven Bueno, Tomasz Frelek, Advikaa Ramesh, Jingyan Bai, Lemeng Wang, Zanming Huang, Jianyang Gu, Jinsu Yoo, Tai-Yu Pan, Arpita Chowdhury, Michelle Ramirez, Elizabeth G. Campolongo, Matthew J. Thompson, Christopher G. Lawrence, Sydne Record, Neil Rosser, Anuj Karpatne, Daniel I. Rubenstein, Hilmar Lapp, Charles V. Stewart, Tanya Y. Berger-Wolf, Yu Su, Wei-Lun Chao

CoRR, January, 2025

OmniMesh: Addressing Findability Challenges in Distributed Nature Data Repositories.

Arnab Nandi, Wei-Lun Chao, Rongjun Qin, Carl Boettiger, Hilmar Lapp, Tanya Y. Berger-Wolf

Proceedings of the 37th International Conference on Scalable Scientific Data Management, 2025

What Do You See in Common? Learning Hierarchical Prototypes over Tree-of-Life to Discover Evolutionary Traits.

Harish Babu Manogaran, M. Maruf, Arka Daw, Kazi Sajeed Mehrab, Caleb Patrick Charpentier, Josef C. Uyeda, Wasila M. Dahdul, Matthew J. Thompson, Elizabeth G. Campolongo, Kaiya L. Provost, Wei-Lun Chao, Tanya Y. Berger-Wolf, Paula M. Mabee, Hilmar Lapp, Anuj Karpatne

Proceedings of the Thirteenth International Conference on Learning Representations, 2025

Fish-Vista: A Multi-Purpose Dataset for Understanding & Identification of Traits from Images.

Kazi Sajeed Mehrab, M. Maruf, Arka Daw, Abhilash Neog, Harish Babu Manogaran, Mridul Khurana, Zhenyang Feng, Bahadir Altintas, Yasin Bakis, Elizabeth G. Campolongo, Matthew J. Thompson, Xiaojun Wang, Hilmar Lapp, Tanya Y. Berger-Wolf, Paula M. Mabee, Henry L. Bart Jr., Wei-Lun Chao, Wasila M. Dahdul, Anuj Karpatne

Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, 2025

2024

What Do You See in Common? Learning Hierarchical Prototypes over Tree-of-Life to Discover Evolutionary Traits.

Harish Babu Manogaran, M. Maruf, Arka Daw, Kazi Sajeed Mehrab, Caleb Charpentier, Josef C. Uyeda, Wasila M. Dahdul, Matthew J. Thompson, Elizabeth G. Campolongo, Kaiya Provost, Paula M. Mabee, Hilmar Lapp, Anuj Karpatne

CoRR, 2024

Fish-Vista: A Multi-Purpose Dataset for Understanding & Identification of Traits from Images.

Kazi Sajeed Mehrab, M. Maruf, Arka Daw, Harish Babu Manogaran, Abhilash Neog, Mridul Khurana, Bahadir Altintas, Yasin Bakis, Elizabeth G. Campolongo, Matthew J. Thompson, Xiaojun Wang, Hilmar Lapp, Wei-Lun Chao, Paula M. Mabee, Henry L. Bart Jr., Wasila M. Dahdul, Anuj Karpatne

CoRR, 2024

VLM4Bio: A Benchmark Dataset to Evaluate Pretrained Vision-Language Models for Trait Discovery from Biological Images.

M. Maruf, Arka Daw, Kazi Sajeed Mehrab, Harish Babu Manogaran, Abhilash Neog, Medha Sawhney, Mridul Khurana, James P. Balhoff, Yasin Bakis, Bahadir Altintas, Matthew J. Thompson, Elizabeth G. Campolongo, Josef C. Uyeda, Hilmar Lapp, Henry L. Bart Jr., Paula M. Mabee, Yu Su, Wei-Lun Chao, Charles V. Stewart, Tanya Y. Berger-Wolf, Wasila M. Dahdul, Anuj Karpatne

Proceedings of the Advances in Neural Information Processing Systems 38: Annual Conference on Neural Information Processing Systems 2024, 2024

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

Mridul Khurana, Arka Daw, M. Maruf, Josef C. Uyeda, Wasila M. Dahdul, Caleb Charpentier, Yasin Bakis, Henry L. Bart Jr., Paula M. Mabee, Hilmar Lapp, James P. Balhoff, Wei-Lun Chao, Charles V. Stewart, Tanya Y. Berger-Wolf, Anuj Karpatne

Proceedings of the Computer Vision - ECCV 2024, 2024

2023

Discovering Novel Biological Traits From Images Using Phylogeny-Guided Neural Networks.

Mohannad Elhamod, Mridul Khurana, Harish Babu Manogaran, Josef C. Uyeda, Meghan A. Balk, Wasila M. Dahdul, Yasin Bakis, Henry L. Bart Jr., Paula M. Mabee, Hilmar Lapp, James P. Balhoff, Caleb Charpentier, David Carlyn, Wei-Lun Chao, Charles V. Stewart, Daniel I. Rubenstein, Tanya Y. Berger-Wolf, Anuj Karpatne

Proceedings of the 29th ACM SIGKDD Conference on Knowledge Discovery and Data Mining, 2023

2021

JPhyloRef: a tool for testing and resolving phyloreferences.

Gaurav Vaidya, Nico Cellinese, Hilmar Lapp

J. Open Source Softw., 2021

Seed Patterns for Modeling Trees.

Aaron Eberhart, David Carral, Pascal Hitzler, Hilmar Lapp, Sebastian Rudolph

Proceedings of the Advances in Pattern-Based Ontology Engineering, 2021

2020

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

Stephen K. Woody, David Burdick, Hilmar Lapp, Erich S. Huang

npj Digit. Medicine, 2020

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

Stephen K. Woody, David Burdick, Hilmar Lapp, Erich S. Huang

npj Digit. Medicine, 2020

2018

Phenoscape: Semantic analysis of organismal traits and genes yields insights in evolutionary biology.

Paula M. Mabee, Wasila M. Dahdul, James P. Balhoff, Hilmar Lapp, Prashanti Manda, Josef C. Uyeda, Todd J. Vision, Monte Westerfield

Proceedings of the Application of Semantic Technology in Biodiversity Science, 2018

'Computable' Phenotypes Enable Comparative and Predictive Phenomics Among Plant Species and Across Domains of Life.

Ian Braun, James P. Balhoff, Tanya Z. Berardini, Laurel Cooper, Georgios V. Gkoutos, Lisa C. Harper, Eva Huala, Pankaj Jaiswal, Toni Kazic, Hilmar Lapp, James A. Macklin, Chelsea D. Specht, Todd J. Vision, Ramona L. Walls, Carolyn J. Lawrence-Dill

Proceedings of the Application of Semantic Technology in Biodiversity Science, 2018

The 2018 Bioinformatics Open Source Conference (GCCBOSC 2018).

Nomi L. Harris, Heather Wiencko, Brad Chapman, Peter J. A. Cock, Karsten Hokamp, Hilmar Lapp, Christopher J. Fields, Bastian Greshake Tzovaras

F1000Research, 2018

Annotation of phenotypes using ontologies: a gold standard for the training and evaluation of natural language processing systems.

Wasila M. Dahdul, Prashanti Manda, Hong Cui, James P. Balhoff, T. Alexander Dececchi, Nizar Ibrahim, Hilmar Lapp, Todd J. Vision, Paula M. Mabee

Database J. Biol. Databases Curation, 2018

Reasoning over Anatomical Homology in the Phenoscape KB.

Paula M. Mabee, James P. Balhoff, Wasila M. Dahdul, Hilmar Lapp, Christopher J. Mungall, Todd J. Vision

Proceedings of the 9th International Conference on Biological Ontology (ICBO 2018), 2018

2017

Community and Code: Nine Lessons from Nine NESCent Hackathons.

Arlin Stoltzfus, Michael S. Rosenberg, Hilmar Lapp, Aidan Budd, Karen Cranston, Enrico Pontelli, Shann Oliver, Rutger A. Vos

F1000Research, 2017

The 2017 Bioinformatics Open Source Conference (BOSC).

Nomi L. Harris, Peter J. A. Cock, Brad Chapman, Christopher J. Fields, Karsten Hokamp, Hilmar Lapp, Monica C. Munoz-Torres, Bastian Greshake Tzovaras, Heather Wiencko

F1000Research, 2017

On the Ontological Modeling of Trees.

David Carral, Pascal Hitzler, Hilmar Lapp, Sebastian Rudolph

Proceedings of the 8th Workshop on Ontology Design and Patterns (WOP 2017) co-located with the 16th International Semantic Web Conference (ISWC 2017), 2017

2016

The 2015 Bioinformatics Open Source Conference (BOSC 2015).

Nomi L. Harris, Peter J. A. Cock, Hilmar Lapp, Brad Chapman, Rob Davey, Christopher J. Fields, Karsten Hokamp, Monica C. Munoz-Torres

PLoS Comput. Biol., 2016

The 2016 Bioinformatics Open Source Conference (BOSC).

Nomi L. Harris, Peter J. A. Cock, Brad Chapman, Christopher J. Fields, Karsten Hokamp, Hilmar Lapp, Monica C. Munoz-Torres, Heather Wiencko

F1000Research, 2016

Investigating the Importance of Anatomical Homology for Cross-Species Phenotype Comparisons Using Semantic Similarity.

Prashanti Manda, Christopher J. Mungall, James P. Balhoff, Hilmar Lapp, Todd J. Vision

Proceedings of the Biocomputing 2016: Proceedings of the Pacific Symposium, 2016

2015

The Bioinformatics Open Source Conference (BOSC) 2013.

Nomi L. Harris, Peter J. A. Cock, Brad A. Chapman, Jeremy Goecks, Hans-Rudolf Hotz, Hilmar Lapp

Bioinform., 2015

Moving the mountain: analysis of the effort required to transform comparative anatomy into computable anatomy.

Wasila M. Dahdul, T. Alexander Dececchi, Nizar Ibrahim, Hilmar Lapp, Paula M. Mabee

Database J. Biol. Databases Curation, 2015

2014

Summary of the First Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE1).

Daniel S. Katz, Sou-Cheng T. Choi, Hilmar Lapp, Ketan Maheshwari, Frank Löffler, Matthew Turk, Marcus D. Hanwell, Nancy Wilkins-Diehr, James Hetherington, James Howison, Shel Swenson, Gabrielle Allen, Anne C. Elster, G. Bruce Berriman, Colin C. Venters

CoRR, 2014

Presence-absence reasoning for evolutionary phenotypes.

James P. Balhoff, T. Alexander Dececchi, Paula M. Mabee, Hilmar Lapp

CoRR, 2014

Annotation of phenotypic diversity: decoupling data curation and ontology curation using Phenex.

James P. Balhoff, Wasila M. Dahdul, Thomas Dececchi, Hilmar Lapp, Paula M. Mabee, Todd J. Vision

J. Biomed. Semant., 2014

2013

Software Engineering as Instrumentation for the Long Tail of Scientific Software.

Daisie Huang, Hilmar Lapp

CoRR, 2013

Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient.

Arlin Stoltzfus, Hilmar Lapp, Naim Matasci, Helena F. Deus, Brian Sidlauskas, Christian M. Zmasek, Gaurav Vaidya, Enrico Pontelli, Karen Cranston, Rutger A. Vos, Campbell O. Webb, Luke J. Harmon, Meg Pirrung, Brian C. O'Meara, Matthew W. Pennell, Siavash Mirarab, Michael S. Rosenberg, James P. Balhoff, Holly M. Bik, Tracy A. Heath, Peter E. Midford, Joseph W. Brown, Emily Jane McTavish, Jeet Sukumaran, Mark Westneat, Michael E. Alfaro, Aaron Steele, Greg Jordan

BMC Bioinform., 2013

The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes.

Peter E. Midford, Thomas Dececchi, James P. Balhoff, Wasila M. Dahdul, Nizar Ibrahim, Hilmar Lapp, John G. Lundberg, Paula M. Mabee, Paul C. Sereno, Monte Westerfield, Todd J. Vision, David C. Blackburn

J. Biomed. Semant., 2013

2012

The <i>PLOS Computational Biology</i> Software Section.

Andreas Prlic, Hilmar Lapp

PLoS Comput. Biol., 2012

2011

The Chado Natural Diversity module: a new generic database schema for large-scale phenotyping and genotyping data.

Sook Jung, Naama Menda, Seth Redmond, Robert M. Buels, Maren Friesen, Yuri R. Bendaña, Lacey-Anne Sanderson, Hilmar Lapp, Taein Lee, Bob MacCallum, Kirstin E. Bett, Scott Cain, Dave Clements, Lukas A. Mueller, Dorrie Main

Database J. Biol. Databases Curation, 2011

Similarity Between Semantic Description Sets: Addressing Needs Beyond Data Integration.

Todd J. Vision, Judith A. Blake, Hilmar Lapp, Paula M. Mabee, Monte Westerfield

Proceedings of the First International Workshop on Linked Science 2011, 2011

Phenoscape: Use Cases and Anatomy Ontology Requirements for Linking Evolutionary and Model Organism Phenotypes.

Wasila M. Dahdul, James P. Balhoff, Hilmar Lapp, Peter E. Midford, Todd J. Vision, Monte Westerfield, Paula M. Mabee

Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

Integrating Anatomy and Phenotype Ontologies with Taxonomic Hierarchies.

James P. Balhoff, Peter E. Midford, Hilmar Lapp

Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

Employing Reasoning within the Phenoscape Knowledgebase.

James P. Balhoff, Wasila M. Dahdul, Hilmar Lapp, Peter E. Midford, Todd J. Vision, Monte Westerfield, Paula M. Mabee

Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

2010

The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows.

Toshiaki Katayama, Kazuharu Arakawa, Mitsuteru Nakao, Keiichiro Ono, Kiyoko F. Aoki-Kinoshita, Yasunori Yamamoto, Atsuko Yamaguchi, Shuichi Kawashima, Hong-Woo Chun, Jan Aerts, Bruno Aranda, Lord H. Barboza, Raoul Jean Pierre Bonnal, Richard M. Bruskiewich, Jan Christian Bryne, José María Fernández, Akira Funahashi, Paul M. K. Gordon, Naohisa Goto, Andreas Groscurth, Alex Gutteridge, Richard C. G. Holland, Yoshinobu Kano, Edward A. Kawas, Arnaud Kerhornou, Eri Kibukawa, Akira R. Kinjo, Michael Kuhn, Hilmar Lapp, Heikki Lehväslaiho, Hiroyuki Nakamura, Yasukazu Nakamura, Tatsuya Nishizawa, Chikashi Nobata, Tamotsu Noguchi, Thomas M. Oinn, Shinobu Okamoto, Stuart Owen, Evangelos Pafilis, Matthew R. Pocock, Pjotr Prins, René Ranzinger, Florian Reisinger, Lukasz Salwínski, Mark J. Schreiber, Martin Senger, Yasumasa Shigemoto, Daron M. Standley, Hideaki Sugawara, Toshiyuki Tashiro, Oswaldo Trelles, Rutger A. Vos, Mark D. Wilkinson, William S. York, Christian M. Zmasek, Kiyoshi Asai, Toshihisa Takagi

J. Biomed. Semant., 2010

2006

Open source tools and toolkits for bioinformatics: significance, and where are we?

Jason E. Stajich, Hilmar Lapp

Briefings Bioinform., 2006

2003

Robust DNA microarray image analysis.

Norbert Brändle, Horst Bischof, Hilmar Lapp

Mach. Vis. Appl., 2003

2000

Robust Parametric and Semi-Parametric Spot Fitting for Spot Array Images.

Norbert Brändle, Horng-Yang Chen, Horst Bischof, Hilmar Lapp

Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology, 2000

Robust Spot Fitting for Genetic Spot Array Images.

Horng-Yang Chen, Norbert Brändle, Horst Bischof, Hilmar Lapp

Proceedings of the 2000 International Conference on Image Processing, 2000

1999

Automatic Grid Fitting for Genetic Spot Array Images Containing Guide Spots.

Norbert Brändle, Hilmar Lapp, Horst Bischof

Proceedings of the Computer Analysis of Images and Patterns, 8th International Conference, 1999