| @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} |
| } |