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2020 – today
- 2024
[j26]Moritz Wolter, Felix Blanke, Jochen Garcke, Charles Tapley Hoyt:
ptwt - The PyTorch Wavelet Toolbox. J. Mach. Learn. Res. 25: 80:1-80:7 (2024)- [d3]Vinay Srinivas Bharadhwaj
, Mehdi Ali, Colin Birkenbihl, Sarah Mubeen, Jens Lehmann, Martin Hofmann-Apitius, Charles Tapley Hoyt, Daniel Domingo-Fernández:
CLEP. Zenodo, 2024
- 2023
- [j25]Charles Tapley Hoyt, Amelia L. Hoyt, Benjamin M. Gyori:
Prediction and curation of missing biomedical identifier mappings with Biomappings. Bioinform. 39(4) (2023) - [j24]Sara Mohammad Taheri, Vartika Tewari, Rohan Kapre, Ehsan Rahiminasab, Karen Sachs, Charles Tapley Hoyt, Jeremy Zucker, Olga Vitek:
Optimal adjustment sets for causal query estimation in partially observed biomolecular networks. Bioinform. 39(Supplement-1): 494-503 (2023) - [j23]Charles Tapley Hoyt, Barbara Zdrazil, Rajarshi Guha, Nina Jeliazkova, Karina Martínez-Mayorga, Eva Nittinger:
Improving reproducibility and reusability in the Journal of Cheminformatics. J. Cheminformatics 15(1): 62 (2023) - [c8]Nicolas Matentzoglu, Ian Braun, Anita R. Caron, Damien Goutte-Gattat, Benjamin M. Gyori, Nomi L. Harris, Emily Hartley, Harshad B. Hegde, Sven Hertling, Charles Tapley Hoyt, Hyeongsik Kim, Huanyu Li, James A. McLaughlin, Cássia Trojahn, Nicole A. Vasilevsky, Christopher J. Mungall:
A simple standard for ontological mappings 2023: updates on data model, collaborations and tooling. OM@ISWC 2023: 73-78 - [i14]Tiffany J. Callahan, Ignacio J. Tripodi, Adrianne L. Stefanski, Luca Cappelletti, Sanya Bathla Taneja, Jordan M. Wyrwa, Elena Casiraghi, Nicolas A. Matentzoglu, Justin T. Reese, Jonathan C. Silverstein, Charles Tapley Hoyt, Richard D. Boyce, Scott A. Malec, Deepak R. Unni, Marcin P. Joachimiak, Peter N. Robinson, Christopher J. Mungall, Emanuele Cavalleri, Tommaso Fontana, Giorgio Valentini, Marco Mesiti, Lucas A. Gillenwater, Brook E. Santangelo, Nicole A. Vasilevsky, Robert Hoehndorf, Tellen D. Bennett, Patrick B. Ryan, George Hripcsak, Michael G. Kahn, Michael Bada, William A. Baumgartner Jr., Lawrence E. Hunter:
An Open-Source Knowledge Graph Ecosystem for the Life Sciences. CoRR abs/2307.05727 (2023) - 2022
- [j22]Stephen Bonner, Ian P. Barrett, Cheng Ye, Rowan Swiers, Ola Engkvist, Andreas Bender, Charles Tapley Hoyt, William L. Hamilton:
A review of biomedical datasets relating to drug discovery: a knowledge graph perspective. Briefings Bioinform. 23(6) (2022) - [j21]Nicolas Matentzoglu, James P. Balhoff, Susan M. Bello, Chris Bizon, Matthew H. Brush, Tiffany J. Callahan, Christopher G. Chute, William D. Duncan, Chris T. A. Evelo, Davera Gabriel, John Graybeal, Alasdair J. G. Gray, Benjamin M. Gyori, Melissa A. Haendel, Henriette Harmse, Nomi L. Harris, Ian Harrow, Harshad Hegde, Amelia L. Hoyt, Charles Tapley Hoyt, Dazhi Jiao, Ernesto Jiménez-Ruiz, Simon Jupp, Hyeongsik Kim, Sebastian Köhler, Thomas Liener, Qinqin Long, James Malone, James A. McLaughlin, Julie A. McMurry, Sierra A. T. Moxon, Monica C. Munoz-Torres, David Osumi-Sutherland, James A. Overton, Bjoern Peters, Tim E. Putman, Núria Queralt-Rosinach, Kent A. Shefchek, Harold Solbrig, Anne E. Thessen, Tania Tudorache, Nicole A. Vasilevsky, Alex H. Wagner, Christopher J. Mungall:
A Simple Standard for Sharing Ontological Mappings (SSSOM). Database J. Biol. Databases Curation 2022(2022) (2022) - [j20]Nicolas Matentzoglu, Damien Goutte-Gattat, Shawn Zheng Kai Tan, James P. Balhoff, Seth Carbon, Anita R. Caron, William D. Duncan, Joe E. Flack, Melissa A. Haendel, Nomi L. Harris, William R. Hogan, Charles Tapley Hoyt, Rebecca C. Jackson, Hyeongsik Kim, Hüseyin Kir, Martin Larralde, Julie A. McMurry, James A. Overton, Bjoern Peters, Clare Pilgrim, Raymund Stefancsik, Sofia M. C. Robb, Sabrina Toro, Nicole A. Vasilevsky, Ramona L. Walls, Christopher J. Mungall, David Osumi-Sutherland:
Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies. Database J. Biol. Databases Curation 2022(2022) (2022) - [j19]Helena Balabin, Charles Tapley Hoyt, Colin Birkenbihl, Benjamin M. Gyori, John A. Bachman, Alpha Tom Kodamullil, Paul G. Plöger, Martin Hofmann-Apitius, Daniel Domingo-Fernández:
STonKGs: a sophisticated transformer trained on biomedical text and knowledge graphs. Bioinform. 38(6): 1648-1656 (2022) - [j18]Benjamin M. Gyori, Charles Tapley Hoyt:
PyBioPAX: biological pathway exchange in Python. J. Open Source Softw. 7(71): 4136 (2022) - [j17]Mehdi Ali, Max Berrendorf, Charles Tapley Hoyt, Laurent Vermue, Mikhail Galkin, Sahand Sharifzadeh, Asja Fischer, Volker Tresp, Jens Lehmann:
Bringing Light Into the Dark: A Large-Scale Evaluation of Knowledge Graph Embedding Models Under a Unified Framework. IEEE Trans. Pattern Anal. Mach. Intell. 44(12): 8825-8845 (2022) - [j16]Ozlem Muslu, Charles Tapley Hoyt, Mauricio Lacerda, Martin Hofmann-Apitius, Holger Fröhlich:
GuiltyTargets: Prioritization of Novel Therapeutic Targets With Network Representation Learning. IEEE ACM Trans. Comput. Biol. Bioinform. 19(1): 491-500 (2022) - [c7]Benedek Rozemberczki, Charles Tapley Hoyt, Anna Gogleva, Piotr Grabowski, Klas Karis, Andrej Lamov, Andriy Nikolov, Sebastian Nilsson, Michaël Ughetto, Yu Wang, Tyler Derr, Benjamin M. Gyori:
ChemicalX: A Deep Learning Library for Drug Pair Scoring. KDD 2022: 3819-3828 - [c6]Nicolas Matentzoglu, Joe E. Flack, John Graybeal, Nomi L. Harris, Harshad B. Hegde, Charles Tapley Hoyt, Hyeongsik Kim, Sabrina Toro, Nicole A. Vasilevsky, Christopher J. Mungall:
A simple standard for ontological mappings 2022: updates of data model and outlook. OM@ISWC 2022: 61-66 - [c5]Helena Balabin, Charles Tapley Hoyt, Benjamin M. Gyori, John A. Bachman, Alpha Tom Kodamullil, Martin Hofmann-Apitius, Daniel Domingo-Fernández:
ProtSTonKGs: A Sophisticated Transformer Trained on Protein Sequences, Text, and Knowledge Graphs. SWAT4HCLS 2022: 103-107 - [d2]Daniel Obraczka, Max Berrendorf, Charles Tapley Hoyt, Michael Galkin, Erhard Rahm:
Benchmark Datasets for Inductive Entity Alignment. Version v0.1.0. Zenodo, 2022 [all versions] - [d1]Daniel Obraczka, Max Berrendorf, Charles Tapley Hoyt, Michael Galkin, Erhard Rahm:
Benchmark Datasets for Inductive Entity Alignment. Version v0.1.1. Zenodo, 2022 [all versions] - [i13]Benedek Rozemberczki, Charles Tapley Hoyt, Anna Gogleva, Piotr Grabowski, Klas Karis, Andrej Lamov, Andriy Nikolov, Sebastian Nilsson, Michaël Ughetto, Yu Wang, Tyler Derr, Benjamin M. Gyori:
ChemicalX: A Deep Learning Library for Drug Pair Scoring. CoRR abs/2202.05240 (2022) - [i12]Mikhail Galkin, Max Berrendorf, Charles Tapley Hoyt:
An Open Challenge for Inductive Link Prediction on Knowledge Graphs. CoRR abs/2203.01520 (2022) - [i11]Charles Tapley Hoyt, Max Berrendorf, Mikhail Galkin, Volker Tresp, Benjamin M. Gyori:
A Unified Framework for Rank-based Evaluation Metrics for Link Prediction in Knowledge Graphs. CoRR abs/2203.07544 (2022) - [i10]Nicolas Matentzoglu, Damien Goutte-Gattat, Shawn Zheng Kai Tan, James P. Balhoff, Seth Carbon, Anita R. Caron, William D. Duncan, Joe E. Flack, Melissa A. Haendel, Nomi L. Harris, William R. Hogan, Charles Tapley Hoyt, Rebecca C. Jackson, Hyeongsik Kim, Hüseyin Kir, Martin Larralde, Julie A. McMurry, James A. Overton, Bjoern Peters, Clare Pilgrim, Raymund Stefancsik, Sofia M. C. Robb, Sabrina Toro, Nicole A. Vasilevsky, Ramona L. Walls, Christopher J. Mungall, David Osumi-Sutherland:
Ontology Development Kit: a toolkit for building, maintaining, and standardising biomedical ontologies. CoRR abs/2207.02056 (2022) - 2021
- [j15]Vasundra Touré, Steven Vercruysse, Marcio Luis Acencio, Ruth C. Lovering, Sandra E. Orchard, Glyn Bradley, Cristina Casals-Casas, Claudine Chaouiya, Noemi del-Toro, Åsmund Flobak, Pascale Gaudet, Henning Hermjakob, Charles Tapley Hoyt, Luana Licata, Astrid Lægreid, Christopher J. Mungall, Anne Niknejad, Simona Panni, Livia Perfetto, Pablo Porras, Dexter Pratt, Julio Saez-Rodriguez, Denis Thieffry, Paul D. Thomas, Dénes Türei, Martin Kuiper:
The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST). Bioinform. 36(24): 5712-5718 (2021) - [j14]Vinay Srinivas Bharadhwaj, Mehdi Ali, Colin Birkenbihl, Sarah Mubeen, Jens Lehmann, Martin Hofmann-Apitius, Charles Tapley Hoyt, Daniel Domingo-Fernández:
CLEP: a hybrid data- and knowledge-driven framework for generating patient representations. Bioinform. 37(19): 3311-3318 (2021) - [j13]Mehdi Ali, Max Berrendorf, Charles Tapley Hoyt, Laurent Vermue, Sahand Sharifzadeh, Volker Tresp, Jens Lehmann:
PyKEEN 1.0: A Python Library for Training and Evaluating Knowledge Graph Embeddings. J. Mach. Learn. Res. 22: 82:1-82:6 (2021) - [j12]Jeremy Leipzig, Daniel Nüst, Charles Tapley Hoyt, Karthik Ram, Jane Greenberg:
The role of metadata in reproducible computational research. Patterns 2(9): 100322 (2021) - [j11]Jeremy Zucker, Kaushal Paneri, Sara Mohammad Taheri, Somya Bhargava, Pallavi Kolambkar, Craig Bakker, Jeremy Teuton, Charles Tapley Hoyt, Kristie L. Oxford, Robert Osazuwa Ness, Olga Vitek:
Leveraging Structured Biological Knowledge for Counterfactual Inference: A Case Study of Viral Pathogenesis. IEEE Trans. Big Data 7(1): 25-37 (2021) - [i9]Jeremy Zucker, Kaushal Paneri, Sara Mohammad Taheri, Somya Bhargava, Pallavi Kolambkar, Craig Bakker, Jeremy Teuton, Charles Tapley Hoyt, Kristie L. Oxford, Robert Osazuwa Ness, Olga Vitek:
Leveraging Structured Biological Knowledge for Counterfactual Inference: a Case Study of Viral Pathogenesis. CoRR abs/2101.05136 (2021) - [i8]Moritz Wolter, Felix Blanke, Charles Tapley Hoyt, Jochen Garcke:
Wavelet-Packet Powered Deepfake Image Detection. CoRR abs/2106.09369 (2021) - [i7]Nicolas Matentzoglu, James P. Balhoff, Susan M. Bello, Chris Bizon, Matthew H. Brush, Tiffany J. Callahan, Christopher G. Chute, William D. Duncan, Chris T. A. Evelo, Davera Gabriel, John Graybeal, Alasdair J. G. Gray, Benjamin M. Gyori, Melissa A. Haendel, Henriette Harmse, Nomi L. Harris, Ian Harrow, Harshad Hegde, Amelia L. Hoyt, Charles Tapley Hoyt, Dazhi Jiao, Ernesto Jiménez-Ruiz, Simon Jupp, Hyeongsik Kim, Sebastian Köhler, Thomas Liener, Qinqin Long, James Malone, James A. McLaughlin, Julie A. McMurry, Sierra A. T. Moxon, Monica C. Munoz-Torres, David Osumi-Sutherland, James A. Overton, Bjoern Peters, Tim E. Putman, Núria Queralt-Rosinach, Kent A. Shefchek, Harold Solbrig, Anne E. Thessen, Tania Tudorache, Nicole A. Vasilevsky, Alex H. Wagner, Christopher J. Mungall:
A Simple Standard for Sharing Ontological Mappings (SSSOM). CoRR abs/2112.07051 (2021) - 2020
- [j10]Mohammad Asif Emon, Daniel Domingo-Fernández, Charles Tapley Hoyt, Martin Hofmann-Apitius:
PS4DR: a multimodal workflow for identification and prioritization of drugs based on pathway signatures. BMC Bioinform. 21(1): 231 (2020) - [j9]Russell J. Bradford, James H. Davenport, Matthew England, Hassan Errami, Vladimir P. Gerdt, Dima Grigoriev, Charles Tapley Hoyt, Marek Kosta, Ovidiu Radulescu, Thomas Sturm, Andreas Weber:
Identifying the parametric occurrence of multiple steady states for some biological networks. J. Symb. Comput. 98: 84-119 (2020) - [i6]Mehdi Ali, Hajira Jabeen, Charles Tapley Hoyt, Jens Lehmann:
The KEEN Universe: An Ecosystem for Knowledge Graph Embeddings with a Focus on Reproducibility and Transferability. CoRR abs/2001.10560 (2020) - [i5]Jeremy Leipzig, Daniel Nüst, Charles Tapley Hoyt, Stian Soiland-Reyes, Karthik Ram, Jane Greenberg:
The role of metadata in reproducible computational research. CoRR abs/2006.08589 (2020) - [i4]Mehdi Ali, Max Berrendorf, Charles Tapley Hoyt, Laurent Vermue, Mikhail Galkin, Sahand Sharifzadeh, Asja Fischer, Volker Tresp, Jens Lehmann:
Bringing Light Into the Dark: A Large-scale Evaluation of Knowledge Graph Embedding Models Under a Unified Framework. CoRR abs/2006.13365 (2020) - [i3]Mehdi Ali, Max Berrendorf, Charles Tapley Hoyt, Laurent Vermue, Sahand Sharifzadeh, Volker Tresp, Jens Lehmann:
PyKEEN 1.0: A Python Library for Training and Evaluating Knowledge Graph Embeddings. CoRR abs/2007.14175 (2020)
2010 – 2019
- 2019
- [b1]Charles Tapley Hoyt:
Generation and Applications of Knowledge Graphs in Systems and Networks Biology. University of Bonn, Germany, 2019 - [j8]Charles Tapley Hoyt, Daniel Domingo-Fernández, Rana Aldisi, Lingling Xu, Kristian Kolpeja, Sandra Spalek, Esther Wollert, John A. Bachman, Benjamin M. Gyori, Patrick Greene, Martin Hofmann-Apitius:
Re-curation and rational enrichment of knowledge graphs in Biological Expression Language. Database J. Biol. Databases Curation 2019: baz068 (2019) - [j7]Mehdi Ali, Charles Tapley Hoyt, Daniel Domingo-Fernández, Jens Lehmann, Hajira Jabeen:
BioKEEN: a library for learning and evaluating biological knowledge graph embeddings. Bioinform. 35(18): 3538-3540 (2019) - [j6]Daniel Domingo-Fernández, Sarah Mubeen, Josep Marín-Llaó, Charles Tapley Hoyt, Martin Hofmann-Apitius:
PathMe: merging and exploring mechanistic pathway knowledge. BMC Bioinform. 20(1): 243:1-243:12 (2019) - [j5]Reagon Karki, Alpha Tom Kodamullil, Charles Tapley Hoyt, Martin Hofmann-Apitius:
Quantifying mechanisms in neurodegenerative diseases (NDDs) using candidate mechanism perturbation amplitude (CMPA) algorithm. BMC Bioinform. 20(1): 494:1-494:8 (2019) - [c4]Eduardo Brito, Bogdan Georgiev, Daniel Domingo-Fernández, Charles Tapley Hoyt, Christian Bauckhage:
RatVec: A General Approach for Low-dimensional Distributed Vector Representations via Rational Kernels. LWDA 2019: 74-78 - [c3]Mehdi Ali, Hajira Jabeen, Charles Tapley Hoyt, Jens Lehmann:
The KEEN Universe - An Ecosystem for Knowledge Graph Embeddings with a Focus on Reproducibility and Transferability. ISWC (2) 2019: 3-18 - [c2]Mehdi Ali, Charles Tapley Hoyt, Daniel Domingo-Fernández, Jens Lehmann:
Predicting Missing Links Using PyKEEN. ISWC (Satellites) 2019: 245-248 - [i2]Russell J. Bradford, James H. Davenport, Matthew England, Hassan Errami, Vladimir P. Gerdt, Dima Grigoriev, Charles Tapley Hoyt, Marek Kosta, Ovidiu Radulescu, Thomas Sturm, Andreas Weber:
Identifying the Parametric Occurrence of Multiple Steady States for some Biological Networks. CoRR abs/1902.04882 (2019) - 2018
- [j4]Charles Tapley Hoyt, Daniel Domingo-Fernández, Nora Balzer, Anka Güldenpfennig, Martin Hofmann-Apitius:
A systematic approach for identifying shared mechanisms in epilepsy and its comorbidities. Database J. Biol. Databases Curation 2018: bay050 (2018) - [j3]Charles Tapley Hoyt, Daniel Domingo-Fernández, Martin Hofmann-Apitius:
BEL Commons: an environment for exploration and analysis of networks encoded in Biological Expression Language. Database J. Biol. Databases Curation 2018: bay126 (2018) - [j2]Charles Tapley Hoyt, Andrej Konotopez, Christian Ebeling:
PyBEL: a computational framework for Biological Expression Language. Bioinform. 34(4): 703-704 (2018) - [j1]Michaela Gündel, Charles Tapley Hoyt, Martin Hofmann-Apitius:
BEL2ABM: agent-based simulation of static models in Biological Expression Language. Bioinform. 34(13): 2316-2318 (2018) - 2017
- [c1]Russell J. Bradford, James H. Davenport, Matthew England, Hassan Errami, Vladimir P. Gerdt, Dima Grigoriev, Charles Tapley Hoyt, Marek Kosta, Ovidiu Radulescu, Thomas Sturm, Andreas Weber:
A Case Study on the Parametric Occurrence of Multiple Steady States. ISSAC 2017: 45-52 - [i1]Russell J. Bradford, James H. Davenport, Matthew England, Hassan Errami, Vladimir P. Gerdt, Dima Grigoriev, Charles Tapley Hoyt, Marek Kosta, Ovidiu Radulescu, Thomas Sturm, Andreas Weber:
A Case Study on the Parametric Occurrence of Multiple Steady States. CoRR abs/1704.08997 (2017)
Coauthor Index
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