source_extract/reference.bib

@article{egozcue2003isometric,
  title={Isometric logratio transformations for compositional data analysis},
  author={Egozcue, Juan Jos{\'e} and Pawlowsky-Glahn, Vera and Mateu-Figueras, Gl{\`o}ria and Barcelo-Vidal, Carles},
  journal={Mathematical Geology},
  volume={35},
  number={3},
  pages={279--300},
  year={2003},
  publisher={Springer}
}

@article{archibald2024haar,
  title={Haar-Like Wavelets on Hierarchical Trees},
  author={Archibald, Rick and Whitney, Ben},
  journal={Journal of Scientific Computing},
  volume={99},
  number={1},
  pages={3},
  year={2024},
  publisher={Springer}
}

@article{egozcue2016changing,
  title={Changing the reference measure in the simplex and its weighting effects},
  author={Egozcue, Juan Jos{\'e} and Pawlowsky-Glahn, Vera},
  journal={Austrian Journal of Statistics},
  volume={45},
  number={4},
  pages={25--44},
  year={2016}
}

@article{silverman2017phylogenetic,
  title={A phylogenetic transform enhances analysis of compositional microbiota data},
  author={Silverman, Justin D and Washburne, Alex D and Mukherjee, Sayan and David, Lawrence A},
  journal={elife},
  volume={6},
  pages={e21887},
  year={2017},
  publisher={eLife Sciences Publications, Ltd}
}

@article{washburne2017phylogenetic,
  title={Phylogenetic factorization of compositional data yields lineage-level associations in microbiome datasets},
  author={Washburne, Alex D and Silverman, Justin D and Leff, Jonathan W and Bennett, Dominic J and Darcy, John L and Mukherjee, Sayan and Fierer, Noah and David, Lawrence A},
  journal={PeerJ},
  volume={5},
  pages={e2969},
  year={2017},
  publisher={PeerJ Inc.}
}

@article{egozcue2005groups,
  title={Groups of parts and their balances in compositional data analysis},
  author={Egozcue, Juan Jos{\'e} and Pawlowsky-Glahn, Vera},
  journal={Mathematical Geology},
  volume={37},
  number={7},
  pages={795--828},
  year={2005},
  publisher={Springer}
}

@article{davis2024fisher,
  title={Fisher flow matching for generative modeling over discrete data},
  author={Davis, Oscar and Kessler, Samuel and Petrache, Mircea and Ceylan, {\.I}smail {\.I} and Bronstein, Michael and Bose, Avishek J},
  journal={Advances in Neural Information Processing Systems},
  volume={37},
  pages={139054--139084},
  year={2024}
}

@article{williams2025simplex,
  title={Simplex-to-Euclidean Bijections for Categorical Flow Matching},
  author={Williams, Bernardo and Yeom-Song, Victor M and Hartmann, Marcelo and Klami, Arto},
  journal={arXiv preprint arXiv:2510.27480},
  year={2025}
}

@article{aitchison1982statistical,
  title={The statistical analysis of compositional data},
  author={Aitchison, John},
  journal={Journal of the Royal Statistical Society: Series B (Methodological)},
  volume={44},
  number={2},
  pages={139--160},
  year={1982},
  publisher={Wiley Online Library}
}

@article{pawlowsky2001geometric,
  title={Geometric approach to statistical analysis on the simplex},
  author={Pawlowsky-Glahn, Vera and Egozcue, Juan Jos{\'e}},
  journal={Stochastic Environmental Research and Risk Assessment},
  volume={15},
  number={5},
  pages={384--398},
  year={2001},
  publisher={Springer}
}

@article{billheimer2001statistical,
  title={Statistical interpretation of species composition},
  author={Billheimer, Dean and Guttorp, Peter and Fagan, William F},
  journal={Journal of the American Statistical Association},
  volume={96},
  number={456},
  pages={1205--1214},
  year={2001},
  publisher={Taylor \& Francis}
}

@book{greenacre2018compositional,
  title={Compositional data analysis in practice},
  author={Greenacre, Michael},
  year={2018},
  publisher={Chapman and Hall/CRC}
}

@article{gloor2017microbiome,
  title={Microbiome datasets are compositional: and this is not optional},
  author={Gloor, Gregory B and Macklaim, Jean M and Pawlowsky-Glahn, Vera and Egozcue, Juan J},
  journal={Frontiers in Microbiology},
  volume={8},
  pages={2224},
  year={2017},
  publisher={Frontiers Media SA}
}

@article{jackson1997compositional,
  title={Compositional data in community ecology: the paradigm or peril of proportions?},
  author={Jackson, Donald A},
  journal={Ecology},
  volume={78},
  number={3},
  pages={929--940},
  year={1997},
  publisher={Wiley Online Library}
}

@article{weltje2008calibration,
  title={Calibration of XRF core scanners for quantitative geochemical logging of sediment cores: Theory and application},
  author={Weltje, Gert Jan and Tjallingii, Rik},
  journal={Earth and Planetary Science Letters},
  volume={274},
  number={3-4},
  pages={423--438},
  year={2008},
  publisher={Elsevier}
}

@article{harmon2019phylogenetic,
  title={Phylogenetic comparative methods: learning from trees},
  author={Harmon, Luke},
  year={2019},
  publisher={EcoEvoRxiv}
}

@article{hamady2010fast,
  title={Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data},
  author={Hamady, Micah and Lozupone, Catherine and Knight, Rob},
  journal={The ISME Journal},
  volume={4},
  number={1},
  pages={17--27},
  year={2010},
  publisher={Oxford University Press}
}

@article{lancaster1965helmert,
  title={The {Helmert} matrices},
  author={Lancaster, HO},
  journal={The American Mathematical Monthly},
  volume={72},
  number={1},
  pages={4--12},
  year={1965},
  publisher={Taylor \& Francis}
}


@article{lin2014variable,
  title={Variable selection in regression with compositional covariates},
  author={Lin, Wei and Shi, Pixu and Feng, Rui and Li, Hongzhe},
  journal={Biometrika},
  volume={101},
  number={4},
  pages={785--797},
  year={2014},
  publisher={Oxford University Press}
}

@article{mandal2015analysis,
  title={Analysis of composition of microbiomes: a novel method for studying microbial composition},
  author={Mandal, Siddhartha and Van Treuren, Will and White, Richard A and Eggesb{\o}, Merete and Knight, Rob and Peddada, Shyamal D},
  journal={Microbial ecology in health and disease},
  volume={26},
  number={1},
  pages={27663},
  year={2015},
  publisher={Taylor \& Francis}
}

@article{rivera2018balances,
  title={Balances: a new perspective for microbiome analysis},
  author={Rivera-Pinto, Javier and Egozcue, Juan Jose and Pawlowsky-Glahn, Vera and Paredes, Raul and Noguera-Julian, Marc and Calle, M Luz},
  journal={MSystems},
  volume={3},
  number={4},
  pages={10--1128},
  year={2018},
  publisher={American Society for Microbiology 1752 N St., NW, Washington, DC}
}

@article{morton2017balance,
  title={Balance trees reveal microbial niche differentiation},
  author={Morton, James T and Sanders, Jon and Quinn, Robert A and McDonald, Daniel and Gonzalez, Antonio and V{\'a}zquez-Baeza, Yoshiki and Navas-Molina, Jose A and Song, Se Jin and Metcalf, Jessica L and Hyde, Embriette R and others},
  journal={MSystems},
  volume={2},
  number={1},
  pages={e00162--16},
  year={2017},
  publisher={American Society for Microbiology 1752 N St., NW, Washington, DC}
}

@article{washburne2019phylofactorization,
  title={Phylofactorization: a graph partitioning algorithm to identify phylogenetic scales of ecological data},
  author={Washburne, Alex D and Silverman, Justin D and Morton, James T and Becker, Daniel J and Crowley, Daniel and Mukherjee, Sayan and David, Lawrence A and Plowright, Raina K},
  journal={Ecological Monographs},
  volume={89},
  number={2},
  pages={e01353},
  year={2019},
  publisher={Wiley Online Library}
}

@article{buettner2021sccoda,
  title={{scCODA} is a {Bayesian} model for compositional single-cell data analysis},
  author={Buettner, Maren and Ostner, Johannes and Mueller, Christian L and Theis, Fabian J and Schubert, Benjamin},
  journal={Nature Communications},
  volume={12},
  number={1},
  pages={6876},
  year={2021},
  publisher={Nature Publishing Group UK London}
}

@book{brigham1988fast,
  title={The {Fast} {Fourier} {Transform} and {Its} {Applications}},
  author={Brigham, E Oran},
  year={1988},
  publisher={Prentice-Hall, Inc.}
}

@article{mallat2002theory,
  title={A theory for multiresolution signal decomposition: the wavelet representation},
  author={Mallat, Stephane G},
  journal={{IEEE} transactions on pattern analysis and machine intelligence},
  volume={11},
  number={7},
  pages={674--693},
  year={2002},
  publisher={Ieee}
}

@article{pasolli2017accessible,
  title={Accessible, curated metagenomic data through ExperimentHub},
  author={Pasolli, Edoardo and Schiffer, Lucas and Manghi, Paolo and Renson, Audrey and Obenchain, Valerie and Truong, Duy Tin and Beghini, Francesco and Malik, Faizan and Ramos, Marcel and Dowd, Jennifer B and others},
  journal={Nature Methods},
  volume={14},
  number={11},
  pages={1023--1024},
  year={2017},
  publisher={Nature Publishing Group US New York}
}

@article{human2012structure,
  title={Structure, function and diversity of the healthy human microbiome},
    author={{Human Microbiome Project Consortium}},
  journal={Nature},
  volume={486},
  number={7402},
  pages={207--214},
  year={2012},
  publisher={Nature Publishing Group UK London}
}

@article{lin2011polytomy,
  title={Polytomy identification in microbial phylogenetic reconstruction},
  author={Lin, Guan Ning and Zhang, Chao and Xu, Dong},
  journal={BMC systems Biology},
  volume={5},
  number={Suppl 3},
  pages={S2},
  year={2011},
  publisher={Springer}
}


@article{dewhirst2010human,
  title={The human oral microbiome},
  author={Dewhirst, Floyd E and Chen, Tuste and Izard, Jacques and Paster, Bruce J and Tanner, Anne CR and Yu, Wen-Han and Lakshmanan, Abirami and Wade, William G},
  journal={Journal of Bacteriology},
  volume={192},
  number={19},
  pages={5002--5017},
  year={2010},
  publisher={American Society for Microbiology}
}

@article{de2010impact,
  title={Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa},
  author={De Filippo, Carlotta and Cavalieri, Duccio and Di Paola, Monica and Ramazzotti, Matteo and Poullet, Jean Baptiste and Massart, Sebastien and Collini, Silvia and Pieraccini, Giuseppe and Lionetti, Paolo},
  journal={Proceedings of the National Academy of Sciences},
  volume={107},
  number={33},
  pages={14691--14696},
  year={2010},
  publisher={National Academy of Sciences}
}

@article{yatsunenko2012human,
  title={Human gut microbiome viewed across age and geography},
  author={Yatsunenko, Tanya and Rey, Federico E and Manary, Mark J and Trehan, Indi and Dominguez-Bello, Maria Gloria and Contreras, Monica and Magris, Magda and Hidalgo, Glida and Baldassano, Robert N and Anokhin, Andrey P and others},
  journal={Nature},
  volume={486},
  number={7402},
  pages={222--227},
  year={2012},
  publisher={Nature Publishing Group UK London}
}

@article{cai2022integrated,
  title={Integrated metagenomics identifies a crucial role for trimethylamine-producing Lachnoclostridium in promoting atherosclerosis},
  author={Cai, Yuan-Yuan and Huang, Feng-Qing and Lao, Xingzhen and Lu, Yawen and Gao, Xuejiao and Alolga, Raphael N and Yin, Kunpeng and Zhou, Xingchen and Wang, Yun and Liu, Baolin and others},
  journal={NPJ Biofilms and Microbiomes},
  volume={8},
  number={1},
  pages={11},
  year={2022},
  publisher={Nature Publishing Group UK London}
}

@article{liang2020novel,
  title={A novel faecal Lachnoclostridium marker for the non-invasive diagnosis of colorectal adenoma and cancer},
  author={Liang, Jessie Qiaoyi and Li, Tong and Nakatsu, Geicho and Chen, Ying-Xuan and Yau, Tung On and Chu, Eagle and Wong, Sunny and Szeto, Chun Ho and Ng, Siew C and Chan, Francis KL and others},
  journal={Gut},
  volume={69},
  number={7},
  pages={1248--1257},
  year={2020},
  publisher={BMJ Publishing Group}
}

@article{costello2009bacterial,
  title={Bacterial community variation in human body habitats across space and time},
  author={Costello, Elizabeth K and Lauber, Christian L and Hamady, Micah and Fierer, Noah and Gordon, Jeffrey I and Knight, Rob},
  journal={Science},
  volume={326},
  number={5960},
  pages={1694--1697},
  year={2009},
  publisher={American Association for the Advancement of Science}
}

@article{zaura2009defining,
  title={Defining the healthy" core microbiome" of oral microbial communities},
  author={Zaura, Egija and Keijser, Bart JF and Huse, Susan M and Crielaard, Wim},
  journal={BMC microbiology},
  volume={9},
  number={1},
  pages={259},
  year={2009},
  publisher={Springer}
}

@article{arumugam2011enterotypes,
  title={Enterotypes of the human gut microbiome},
  author={Arumugam, Manimozhiyan and Raes, Jeroen and Pelletier, Eric and Le Paslier, Denis and Yamada, Takuji and Mende, Daniel R and Fernandes, Gabriel R and Tap, Julien and Bruls, Thomas and Batto, Jean-Michel and others},
  journal={Nature},
  volume={473},
  number={7346},
  pages={174--180},
  year={2011},
  publisher={Nature Publishing Group UK London}
}

@inproceedings{
    palumbo2025from,
    title={From Logits to Hierarchies: Hierarchical Clustering made Simple},
    author={Emanuele Palumbo and Moritz Vandenhirtz and Alain Ryser and Imant Daunhawer and Julia E Vogt},
    booktitle={Forty-second International Conference on Machine Learning},
    year={2025},
    url={https://openreview.net/forum?id=t0x2VnBskT}
}

@article{lozupone2005unifrac,
  title={UniFrac: a new phylogenetic method for comparing microbial communities},
  author={Lozupone, Catherine and Knight, Rob},
  journal={Applied and environmental microbiology},
  volume={71},
  number={12},
  pages={8228--8235},
  year={2005},
  publisher={American Society for Microbiology}
}

@article{mao2022dirichlet,
  title={{Dirichlet}-tree multinomial mixtures for clustering microbiome compositions},
  author={Mao, Jialiang and Ma, Li},
  journal={The Annals of Applied Statistics},
  volume={16},
  number={3},
  pages={1476},
  year={2022}
}

@article{ashburner2000gene,
  title={Gene ontology: tool for the unification of biology},
  author={Ashburner, Michael and Ball, Catherine A and Blake, Judith A and Botstein, David and Butler, Heather and Cherry, J Michael and Davis, Allan P and Dolinski, Kara and Dwight, Selina S and Eppig, Janan T and others},
  journal={Nature Genetics},
  volume={25},
  number={1},
  pages={25--29},
  year={2000},
  publisher={Nature Publishing Group}
}

@article{rudin2019stop,
  title={Stop explaining black box machine learning models for high stakes decisions and use interpretable models instead},
  author={Rudin, Cynthia},
  journal={Nature Machine Intelligence},
  volume={1},
  number={5},
  pages={206--215},
  year={2019},
  publisher={Nature Publishing Group UK London}
}

@article{marcos2021applications,
  title={Applications of machine learning in human microbiome studies: a review on feature selection, biomarker identification, disease prediction and treatment},
  author={Marcos-Zambrano, Laura Judith and Karaduzovic-Hadziabdic, Kanita and Loncar Turukalo, Tatjana and Przymus, Piotr and Trajkovik, Vladimir and Aasmets, Oliver and Berland, Magali and Gruca, Aleksandra and Hasic, Jasminka and Hron, Karel and others},
  journal={Frontiers in Microbiology},
  volume={12},
  pages={634511},
  year={2021},
  publisher={Frontiers Media SA}
}

@inproceedings{deng2009imagenet,
  title={{ImageNet}: A large-scale hierarchical image database},
  author={Deng, Jia and Dong, Wei and Socher, Richard and Li, Li-Jia and Li, Kai and Fei-Fei, Li},
  booktitle={2009 {IEEE} conference on computer vision and pattern recognition},
  pages={248--255},
  year={2009},
  organization={Ieee}
}

@article{miller1995wordnet,
  title={{WordNet}: a lexical database for {E}nglish},
  author={Miller, George A},
  journal={Communications of the ACM},
  volume={38},
  number={11},
  pages={39--41},
  year={1995},
  publisher={ACM New York, NY, USA}
}

@article{krizhevsky2009learning,
  title={Learning multiple layers of features from tiny images},
  author={Krizhevsky, Alex and Hinton, Geoffrey and others},
  year={2009},
  publisher={Toronto, ON, Canada}
}

@article{kaul2017analysis,
  title={Analysis of microbiome data in the presence of excess zeros},
  author={Kaul, Abhishek and Mandal, Siddhartha and Davidov, Ori and Peddada, Shyamal D},
  journal={Frontiers in microbiology},
  volume={8},
  pages={2114},
  year={2017},
  publisher={Frontiers Media SA}
}

@article{hu2022locom,
  title={{LOCOM}: A logistic regression model for testing differential abundance in compositional microbiome data with false discovery rate control},
  author={Hu, Yingtian and Satten, Glen A and Hu, Yi-Juan},
  journal={Proceedings of the National Academy of Sciences},
  volume={119},
  number={30},
  pages={e2122788119},
  year={2022},
  publisher={National Academy of Sciences}
}

@article{li2022disco,
  title={{DISCO}: a database of Deeply Integrated human Single-Cell Omics data},
  author={Li, Mengwei and Zhang, Xiaomeng and Ang, Kok Siong and Ling, Jingjing and Sethi, Raman and Lee, Nicole Yee Shin and Ginhoux, Florent and Chen, Jinmiao},
  journal={Nucleic acids research},
  volume={50},
  number={D1},
  pages={D596--D602},
  year={2022},
  publisher={Oxford University Press}
}

@article{lowenberg1999acute,
  title={Acute myeloid leukemia},
  author={L{\"o}wenberg, Bob and Downing, James R and Burnett, Alan},
  journal={New England Journal of Medicine},
  volume={341},
  number={14},
  pages={1051--1062},
  year={1999},
  publisher={Mass Medical Soc}
}

@article{sorensen2015liver,
  title={Liver sinusoidal endothelial cells},
  author={S{\o}rensen, Karen Kristine and Simon-Santamaria, Jaione and McCuskey, Robert S and Smedsr{\o}d, B{\aa}rd},
  journal={Comprehensive Physiology},
  volume={5},
  number={4},
  pages={1751--1774},
  year={2015},
  publisher={John Wiley \& Sons, Ltd}
}

@article{phipson2022propeller,
  title={{propeller}: testing for differences in cell type proportions in single cell data},
  author={Phipson, Belinda and Sim, Choon Boon and Porrello, Enzo R and Hewitt, Alex W and Powell, Joseph and Oshlack, Alicia},
  journal={Bioinformatics},
  volume={38},
  number={20},
  pages={4720--4726},
  year={2022},
  publisher={Oxford University Press}
}

@inproceedings{
malashin2025hypernym,
title={Hypernym Bias: Unraveling Deep Classifier Training Dynamics through the Lens of Class Hierarchy},
author={Roman Malashin and Yachnaya Valeria and Alexandr V. Mullin},
booktitle={The 28th International Conference on Artificial Intelligence and Statistics},
year={2025},
url={https://openreview.net/forum?id=DobXzInjnV}
}

@article{nickel2017poincare,
  title={Poincar{\'e} embeddings for learning hierarchical representations},
  author={Nickel, Maximillian and Kiela, Douwe},
  journal={Advances in neural information processing systems},
  volume={30},
  year={2017}
}

@article{chami2019hyperbolic,
  title={Hyperbolic graph convolutional neural networks},
  author={Chami, Ines and Ying, Zhitao and R{\'e}, Christopher and Leskovec, Jure},
  journal={Advances in neural information processing systems},
  volume={32},
  year={2019}
}

@article{billera2001geometry,
  title={Geometry of the space of phylogenetic trees},
  author={Billera, Louis J and Holmes, Susan P and Vogtmann, Karen},
  journal={Advances in Applied Mathematics},
  volume={27},
  number={4},
  pages={733--767},
  year={2001},
  publisher={Elsevier}
}

@article{owen2010fast,
  title={A fast algorithm for computing geodesic distances in tree space},
  author={Owen, Megan and Provan, J Scott},
  journal={IEEE/ACM Transactions on Computational Biology and Bioinformatics},
  volume={8},
  number={1},
  pages={2--13},
  year={2010},
  publisher={IEEE}
}

@article{monod2018tropical,
  title={Tropical geometry of phylogenetic tree space: a statistical perspective},
  author={Monod, Anthea and Lin, Bo and Yoshida, Ruriko and Kang, Qiwen},
  journal={arXiv preprint arXiv:1805.12400},
  year={2018}
}

@article{silla2011survey,
  title={A survey of hierarchical classification across different application domains},
  author={Silla Jr, Carlos N and Freitas, Alex A},
  journal={Data mining and knowledge discovery},
  volume={22},
  number={1},
  pages={31--72},
  year={2011},
  publisher={Springer}
}

@inproceedings{sala2018representation,
  title={Representation tradeoffs for hyperbolic embeddings},
  author={Sala, Frederic and De Sa, Chris and Gu, Albert and R{\'e}, Christopher},
  booktitle={International Conference on Machine Learning},
  pages={4460--4469},
  year={2018},
  organization={PMLR}
}

@article{ma2024systematic,
  title={A systematic framework for understanding the microbiome in human health and disease: from basic principles to clinical translation},
  author={Ma, Ziqi and Zuo, Tao and Frey, Norbert and Rangrez, Ashraf Yusuf},
  journal={Signal Transduction and Targeted Therapy},
  volume={9},
  number={1},
  pages={237},
  year={2024},
  publisher={Nature Publishing Group UK London}
}

@article{maddison1989reconstructing,
  title={Reconstructing character evolution on polytomous cladograms},
  author={Maddison, Wayne},
  journal={Cladistics},
  volume={5},
  number={4},
  pages={365--377},
  year={1989},
  publisher={Wiley Online Library}
}

@article{diehl2016cell,
  title={The {Cell} {Ontology} 2016: enhanced content, modularization, and ontology interoperability},
  author={Diehl, Alexander D and Meehan, Terrence F and Bradford, Yvonne M and Brush, Matthew H and Dahdul, Wasila M and Dougall, David S and He, Yongqun and Osumi-Sutherland, David and Ruttenberg, Alan and Sarntivijai, Sirarat and others},
  journal={Journal of Biomedical Semantics},
  volume={7},
  number={1},
  pages={44},
  year={2016},
  publisher={Springer}
}

@article{pasolli2020large,
  title={Large-scale genome-wide analysis links lactic acid bacteria from food with the gut microbiome},
  author={Pasolli, Edoardo and De Filippis, Francesca and Mauriello, Italia E and Cumbo, Fabio and Walsh, Aaron M and Leech, John and Cotter, Paul D and Segata, Nicola and Ercolini, Danilo},
  journal={Nature Communications},
  volume={11},
  number={1},
  pages={2610},
  year={2020},
  publisher={Nature Publishing Group UK London}
}

@article{yerke2024proportion,
  title={Proportion-based normalizations outperform compositional data transformations in machine learning applications},
  author={Yerke, Aaron and Fry Brumit, Daisy and Fodor, Anthony A},
  journal={Microbiome},
  volume={12},
  number={1},
  pages={45},
  year={2024},
  publisher={Springer}
}