La replicabilidad en la ciencia y el papel transformador de la metodología estadística de knockoffs

Autores/as

  • Alejandro Román Vásquez Departamento de Matemáticas, Universidad Autónoma Metropolitana unidad Iztapalapa
  • Gabriel Escarela Pérez Departamento de Matemáticas, Universidad Autónoma Metropolitana Unidad Iztapalapa
  • Gabriel Núñez-Antonio Departamento de Matemáticas, Universidad Autónoma Metropolitana Unidad Iztapalapa
  • José Ulises Márquez Urbina CONAHCYT - Centro de Investigación en Matemáticas

DOI:

https://doi.org/10.36788/sah.v8i1.148

Palabras clave:

Crisis de replicabilidad, Modelo-X de imitaciones, Hipótesis estadísticas múltiples

Resumen

Un aspecto importante en la ciencia es la replicabilidad de los resultados científicos. En este artículo se examinan algunas causas fundamentales que contribuyen a la falta de replicabilidad, centrando el análisis en un componente crucial: la estadística y la inferencia selectiva. Partiendo de los desafíos inherentes a las pruebas de hipótesis múltiples en situaciones de alta dimensionalidad, una estrategia para abordar la problemática de la replicabilidad se basa en la implementación del modelo-X de imitaciones. Esta metodología se destaca por generar variables sintéticas que imitan a las originales, permitiendo diferenciar de manera efectiva entre asociaciones genuinas y espurias, y controlando de manera simultánea la tasa de falsos descubrimientos en entornos de muestras finitas. Los aspectos técnicos del modelo-X de imitaciones se describen en este trabajo, subrayando sus alcances y limitaciones. Se enfatiza la efectividad de esta metodología con casos de éxito, tales como la estimación de la pureza en tumores, el análisis de asociación genómica, la identificación de factores pronósticos en ensayos clínicos, la determinación de factores de riesgo asociados al COVID-19 de larga duración, y la selección de variables en estudios de tasa de criminalidad. Estos ejemplos concretos ilustran la preponderante utilidad práctica y la versatilidad del modelo-X de imitaciones en diversas áreas de investigación. Sin lugar a dudas, este enfoque contribuye de manera original a los desafíos actuales en cuanto a la replicabilidad, marcando un hito significativo en la mejora de la confiabilidad y robustez de la evidencia científica.

Descargas

Los datos de descargas todavía no están disponibles.

Citas

A. Ahlgren, “A modest proposal for encouraging replication,” American Psychologist, vol. 24, no. 4, p. 471, 1969. DOI: https://doi.org/10.1037//0003-066X.24.4.471.a

R. F. Barber and E. J. Candès, “Controlling the false discovery rate via knockoffs,” The Annals of Statistics, vol. 43, no. 5, pp. 2055 – 2085, 2015. DOI: https://doi.org/10.1214/15-AOS1337

R. F. Barber, E. J. Candès, and R. J. Samworth, “Robust inference with knockoffs,” The Annals of Statistics, vol. 48, no. 3, pp. 1409 – 1431, 2020. DOI: https://doi.org/10.1214/19-AOS1852

J. A. Bargh, M. Chen, and L. Burrows, “Automaticity of social behavior: Direct effects of trait construct and stereotype activation on action.” Journal of personality and social psychology, vol. 71, no. 2, p. 230, 1996. DOI: https://doi.org/10.1037//0022-3514.71.2.230

S. Bates, E. Candès, L. Janson, and W. Wang, “Metropolized knockoff sampling,” Journal of the American Statistical Association, vol. 116, no. 535, pp. 1413–1427, 2021. DOI: https://doi.org/10.1080/01621459.2020.1729163

C. G. Begley and L. M. Ellis, “Raise standards for preclinical cancer research,” Nature, vol. 483, no. 7391, pp. 531–533, 2012. DOI: https://doi.org/10.1038/483531a

D. J. Bem, “Feeling the future: experimental evidence for anomalous retroactive influences on cognition and affect.” Journal of personality and social psychology, vol. 100, no. 3, p. 407, 2011. DOI: https://doi.org/10.1037/a0021524

D. J. Benjamin, J. O. Berger, M. Johannesson, B. A. Nosek, E.-J. Wagenmakers, R. Berk, K. A. Bollen, B. Brembs, L. Brown, C. Camerer et al., “Redefine statistical significance,” Nature human behaviour, vol. 2, no. 1, pp. 6–10, 2018. DOI: https://doi.org/10.1038/s41562-017-0189-z

Y. Benjamini, “Selective Inference: The Silent Killer of Replicability,” Harvard Data Science Review, vol. 2, no. 4, dec 16 2020, https://hdsr.mitpress.mit.edu/pub/l39rpgyc. DOI: https://doi.org/10.1162/99608f92.fc62b261

Y. Benjamini and Y. Hochberg, “Controlling the false discovery rate: a practical and powerful approach to multiple testing,” Journal of the Royal statistical society: series B (Methodological), vol. 57, no. 1, pp. 289–300, 1995. DOI: https://doi.org/10.1111/j.2517-6161.1995.tb02031.x

M. Binkowski, D. J. Sutherland, M. Arbel, and A. Gretton, “Demystifying mmd gans,” arXiv preprint arXiv:1801.01401, 2018.

D. Bishop, “Interpreting unexpected significant findings,” 2014.

F. Bretz, T. Hothorn, and P. Westfall, Multiple comparisons using R. CRC press, 2016. DOI: https://doi.org/10.1201/9781420010909

K. E. Campbell and T. T. Jackson, “The role of and need for replication research in social psychology,” Replications in social psychology, vol. 1, no. 1, pp. 3–14, 1979.

E. Candès, Y. Fan, L. Janson, and J. Lv, “Panning for gold:‘Model-X’ knockoffs for high dimensional controlled variable selection,” Journal of the Royal Statistical Society Series B: Statistical Methodology, vol. 80, no. 3, pp. 551–577, 2018. DOI: https://doi.org/10.1111/rssb.12265

T. Chen and C. Guestrin, “XGBoost: A scalable tree boosting system,” in Proceedings of the 22nd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, 2016, pp. 785–794. DOI: https://doi.org/10.1145/2939672.2939785

J. Cohen, “Things I have learned (so far).” in Annual Convention of the American Psychological Association, 98th, Aug, 1990, Boston, MA, US; Presented at the aforementioned conference. American Psychological Association, 1990.

L. J. Colling and D. Szucs, “Statistical inference and the replication crisis,” Review of Philosophy and Psychology, vol. 12, pp. 121–147, 2021. DOI: https://doi.org/10.1007/s13164-018-0421-4

A. O. Cramer, D. van Ravenzwaaij, D. Matzke, H. Steingroever, R. Wetzels, R. P. Grasman, L. J. Waldorp, and E.-J. Wagenmakers, “Hidden multiplicity in exploratory multiway ANOVA: Prevalence and remedies,” Psychonomic bulletin & review, vol. 23, pp. 640–647, 2016. DOI: https://doi.org/10.3758/s13423-015-0913-5

R. Dai and C. Zheng, “False discovery rate-controlled multiple testing for union null hypotheses: a knockoff-based approach,” Biometrics, 2023. DOI: https://doi.org/10.1111/biom.13848

S. Doyen, O. Klein, C.-L. Pichon, and A. Cleeremans, “Behavioral priming: It’s all in the mind, but whose mind?” PLOS ONE, vol. 7, no. 1, 01 2012. DOI: https://doi.org/10.1371/journal.pone.0029081

F. Fidler et al., “Should psychology abandon p values and teach cis instead? evidence-based reforms in statistics education,” 2006.

E. I. George and R. E. McCulloch, “Approaches for bayesian variable selection,” Statistica Sinica, pp. 339–373, 1997.

I. Gulrajani, F. Ahmed, M. Arjovsky, V. Dumoulin, and A. C. Courville, “Improved training of wasserstein gans,” Advances in neural information processing systems, vol. 30, 2017.

M. A. Haendel, C. G. Chute, T. D. Bennett, D. A. Eichmann, J. Guinney, W. A. Kibbe, P. R. Payne, E. R. Pfaff, P. N. Robinson, J. H. Saltz et al., “The national covid cohort collaborative (n3c): rationale, design, infrastructure, and deployment,” Journal of the American Medical Informatics Association, vol. 28, no. 3, pp. 427–443, 2021. DOI: https://doi.org/10.1093/jamia/ocaa196

J. P. A. Ioannidis, “Why most published research findings are false,” PLOS Medicine, vol. 2, no. 8, 08 2005. DOI: https://doi.org/10.1371/journal.pmed.0020124

T. Jiang, Y. Li, and A. A. Motsinger-Reif, “Knockoff boosted tree for model-free variable selection,” Bioinformatics, vol. 37, no. 7, pp. 976–983, 2021. DOI: https://doi.org/10.1093/bioinformatics/btaa770

J. Jordon, J. Yoon, and M. van der Schaar, “Knockoffgan: Generating knockoffs for feature selection using generative adversarial networks,” in International conference on learning representations, 2018.

M. Kormaksson, L. J. Kelly, X. Zhu, S. Haemmerle, L. Pricop, and D. Ohlssen, “Sequential knockoffs for continuous and categorical predictors: With application to a large psoriatic arthritis clinical trial pool,” Statistics in Medicine, vol. 40, no. 14, pp. 3313–3328, 2021. DOI: https://doi.org/10.1002/sim.8955

E. Lander and L. Kruglyak, “Genetic dissection of complex traits: guidelines for interpreting and reporting linkage results,” Nature genetics, vol. 11, no. 3, pp. 241–247, 1995. DOI: https://doi.org/10.1038/ng1195-241

Y. Li, D. M. Umbach, A. Bingham, Q.-J. Li, Y. Zhuang, and L. Li, “Putative biomarkers for predicting tumor sample purity based on gene expression data,” BMC genomics, vol. 20, no. 1, pp. 1–12, 2019. DOI: https://doi.org/10.1186/s12864-019-6412-8

P.-R. Loh, G. Kichaev, S. Gazal, A. P. Schoech, and A. L. Price, “Mixed-model association for biobank-scale datasets,” Nature genetics, vol. 50, no. 7, pp. 906–908, 2018. DOI: https://doi.org/10.1038/s41588-018-0144-6

Y. Lu, Y. Fan, J. Lv, and W. Stafford Noble, “DeepPINK: reproducible feature selection in deep neural networks,” Advances in neural information processing systems, vol. 31, 2018.

S. M. Lundberg and S.-I. Lee, “A unified approach to interpreting model predictions,” Advances in neural information processing systems, vol. 30, 2017.

C. C. Mann, “Behavioral genetics in transition: A mass of evidence—animal and human—shows that genes influence behavior. but the attempt to pin down which genes influence which behaviors has proved frustratingly difficult,” Science, vol. 264, no. 5166, pp. 1686–1689, 1994. DOI: https://doi.org/10.1126/science.8209246

L. Mescheder, S. Nowozin, and A. Geiger, “The numerics of gans,” Advances in neural information processing systems, vol. 30, 2017.

National Academies of Sciences, Engineering, and Medicine, “Reproducibility and replicability in science,” 2019.

R. Nuzzo, “Scientific method: Statistical errors,” Nature, vol. 506, no. 7487, p. 150, 2014. DOI: https://doi.org/10.1038/506150a

Open Science Collaboration, “Estimating the reproducibility of psychological science,” Science, vol. 349, no. 6251, p. aac4716, 2015. DOI: https://doi.org/10.1126/science.aac4716

H. Pashler, C. Harris, and N. Coburn, “Elderly-related words prime slow walking. psychfiledrawer,” 2011.

F. Prinz, T. Schlange, and K. Asadullah, “Believe it or not: how much can we rely on published data on potential drug targets?” Nature reviews Drug discovery, vol. 10, no. 9, pp. 712–712, 2011. DOI: https://doi.org/10.1038/nrd3439-c1

A. Ramdas, S. J. Reddi, B. Póczos, A. Singh, and L. Wasserman, “On the decreasing power of kernel and distance based nonparametric hypothesis tests in high dimensions,” in Proceedings of the AAAI Conference on Artificial Intelligence, vol. 29, no. 1, 2015. DOI: https://doi.org/10.1609/aaai.v29i1.9692

Z. Ren, Model-free Methods For Multiple Testing and Predictive Inference. Stanford University, 2021.

Y. Romano, M. Sesia, and E. Cand`es, “Deep knockoffs,” Journal of the American Statistical Association, vol. 115, no. 532, pp. 1861–1872, 2020. DOI: https://doi.org/10.1080/01621459.2019.1660174

F. Romero, “Philosophy of science and the replicability crisis,” Philosophy Compass, vol. 14, no. 11, p. e12633, 2019. DOI: https://doi.org/10.1111/phc3.12633

K. Sechidis, M. Kormaksson, and D. Ohlssen, “Using knockoffs for controlled predictive biomarker identification,” Statistics in Medicine, vol. 40, no. 25, pp. 5453–5473, 2021. DOI: https://doi.org/10.1002/sim.9134

M. Sesia, C. Sabatti, and E. J. Cand`es, “Gene hunting with hidden markov model knockoffs,” Biometrika, vol. 106, no. 1, pp. 1–18, 2019. DOI: https://doi.org/10.1093/biomet/asy033

M. Sesia, S. Bates, E. Candès, J. Marchini, and C. Sabatti, “False discovery rate control in genome-wide association studies with population structure,” Proceedings of the National Academy of Sciences, vol. 118, no. 40, p. e2105841118, 2021. DOI: https://doi.org/10.1073/pnas.2105841118

J. P. Simmons, L. D. Nelson, and U. Simonsohn, “False-positive psychology: Undisclosed flexibility in data collection and analysis allows presenting anything as significant,” Psychological science, vol. 22, no. 11, pp. 1359–1366, 2011. DOI: https://doi.org/10.1177/0956797611417632

N. C. Smith, “Replication studies: A neglected aspect of psychological research.” American Psychologist, vol. 25, no. 10, p. 970, 1970. DOI: https://doi.org/10.1037/h0029774

A. Spector and L. Janson, “Powerful knockoffs via minimizing reconstructability,” The Annals of Statistics, vol. 50, no. 1, pp. 252–276, 2022. DOI: https://doi.org/10.1214/21-AOS2104

W. Stroebe, T. Postmes, and R. Spears, “Scientific misconduct and the myth of selfcorrection in science,” Perspectives on psychological science, vol. 7, no. 6, pp. 670–688, 2012. DOI: https://doi.org/10.1177/1745691612460687

M. Sudarshan, W. Tansey, and R. Ranganath, “Deep direct likelihood knockoffs,” Advances in neural information processing systems, vol. 33, pp. 5036–5046, 2020.

P. Sur and E. J. Cand`es, “A modern maximum-likelihood theory for high-dimensional logistic regression,” Proceedings of the National Academy of Sciences, vol. 116, no. 29, pp. 14 516–14 525, 2019. DOI: https://doi.org/10.1073/pnas.1810420116

D. Trafimow and M. Marks, “Editorial,” Basic and Applied Social Psychology, vol. 37, no. 1, pp. 1–2, 2015. DOI: https://doi.org/10.1080/01973533.2015.1012991

A. R. Vásquez, J. U. Márquez Urbina, G. Gonz´alez Far´ıas, and G. Escarela, “Controlling the false discovery rate by a latent gaussian copula knockoff procedure,” Computational Statistics, pp. 1–24, 2023. DOI: https://doi.org/10.1007/s00180-023-01346-4

R. Wang, R. Dai, and C. Zheng, “Controlling fdr in selecting group-level simultaneous signals from multiple data sources with application to the national covid collaborative cohort data,” arXiv preprint arXiv:2303.01599, 2023.

R. L. Wasserstein and N. A. Lazar, “The asa statement on p-values: context, process, and purpose,” pp. 129–133, 2016. DOI: https://doi.org/10.1080/00031305.2016.1154108

R. L. Wasserstein, A. L. Schirm, and N. A. Lazar, “Moving to a world beyond “p¡ 0.05”,”pp. 1–19, 2019.

K. Yoshihara, M. Shahmoradgoli, E. Mart´ınez, R. Vegesna, H. Kim, W. Torres-Garcia, V. Trevi˜no, H. Shen, P. W. Laird, D. A. Levine et al., “Inferring tumour purity and stromal and immune cell admixture from expression data,” Nature communications, vol. 4, no. 1,p. 2612, 2013. DOI: https://doi.org/10.1038/ncomms3612

S. T. Ziliak and D. N. McCloskey, The cult of statistical significance: How the standard error costs us jobs, justice, and lives. University of Michigan Press, 2010.

Descargas

Publicado

2024-06-30

Cómo citar

[1]
A. R. Vásquez, G. Escarela Pérez, G. Núñez-Antonio, y J. U. . Márquez Urbina, «La replicabilidad en la ciencia y el papel transformador de la metodología estadística de knockoffs», sahuarus, vol. 8, n.º 1, pp. 1–22, jun. 2024.

Número

Sección

Artículos

Métrica