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LiPydomics: A Python Package for Comprehensive Prediction of Lipid Collision Cross Sections and Retention Times and Analysis of Ion Mobility-Mass Spectrometry-Based Lipidomics Data by Ross, Dylan H, Cho, Jang Ho, Zhang, Rutan, Hines, Kelly M, Xu, Libin

“… Existing solutions for these data analysis challenges (i.e., multivariate statistics and lipid identification…”
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Introduction to computational causal inference using reproducible Stata, R, and Python code: A tutorial by Smith, Matthew J., Mansournia, Mohammad A., Maringe, Camille, Zivich, Paul N., Cole, Stephen R., Leyrat, Clémence, Belot, Aurélien, Rachet, Bernard, Luque‐Fernandez, Miguel A.

“…The main purpose of many medical studies is to estimate the effects of a treatment or exposure on an outcome. However, it is not always possible to randomize…”
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Decoding the JAK-STAT Axis in Colorectal Cancer with AI-HOPE-JAK-STAT: A Conversational Artificial Intelligence Approach to Clinical–Genomic Integration by Yang, Ei-Wen, Waldrup, Brigette, Velazquez-Villarreal, Enrique

“…: AI-HOPE-JAK-STAT combines large language models (LLMs), a natural language-to-code engine, and harmonized public CRC datasets from cBioPortal…”
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Statistical analysis of feature-based molecular networking results from non-targeted metabolomics data by Pakkir Shah, Abzer K., Walter, Axel, Ottosson, Filip, Russo, Francesco, Navarro-Diaz, Marcelo, Boldt, Judith, Kalinski, Jarmo-Charles J., Kontou, Eftychia Eva, Elofson, James, Polyzois, Alexandros, González-Marín, Carolina, Farrell, Shane, Aggerbeck, Marie R., Pruksatrakul, Thapanee, Chan, Nathan, Wang, Yunshu, Pöchhacker, Magdalena, Brungs, Corinna, Cámara, Beatriz, Caraballo-Rodríguez, Andrés Mauricio, Cumsille, Andres, de Oliveira, Fernanda, Dührkop, Kai, El Abiead, Yasin, Geibel, Christian, Graves, Lana G., Hansen, Martin, Heuckeroth, Steffen, Knoblauch, Simon, Kostenko, Anastasiia, Kuijpers, Mirte C. M., Mildau, Kevin, Papadopoulos Lambidis, Stilianos, Portal Gomes, Paulo Wender, Schramm, Tilman, Steuer-Lodd, Karoline, Stincone, Paolo, Tayyab, Sibgha, Vitale, Giovanni Andrea, Wagner, Berenike C., Xing, Shipei, Yazzie, Marquis T., Zuffa, Simone, de Kruijff, Martinus, Beemelmanns, Christine, Link, Hannes, Mayer, Christoph, van der Hooft, Justin J. J., Damiani, Tito, Pluskal, Tomáš, Dorrestein, Pieter, Stanstrup, Jan, Schmid, Robin, Wang, Mingxun, Aron, Allegra, Ernst, Madeleine, Petras, Daniel

“… We provide explanations and code in two scripting languages (R and Python) as well…”
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Nestedness for Dummies (NeD): A user friendly web interface for exploratory nestedness analysis by Strona, Giovanni, Galli, Paolo, Seveso, Davide, Montano, Simone, Fattorini, Simone

“…Recent theoretical advances in nestedness analysis have led to the introduction of several alternative metrics to overcome most of the problems biasing the use of matrix 'temperature' calculated…”
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Statistical Analyses and Reproducible Research by Gentleman, Robert, Temple Lang, Duncan

“…It is important, if not essential, to integrate the computations and code used in data analyses, methodological descriptions, simulations, and so on with the documents that describe and rely…”
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Facilitating the Calculation of the Efficient Score Using Symbolic Computing by B. Sibley, Alexander, Li, Zhiguo, Jiang, Yu, Li, Yi-Ju, Chan, Cliburn, Allen, Andrew, Owzar, Kouros

“… In the analysis of data from high-throughput genomic assays, inference on the basis of the score usually enjoys greater stability, considerably higher computational efficiency, and lends itself…”
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Using GNU Make to Manage the Workflow of Data Analysis Projects by Baker, Peter

“…Data analysis projects invariably involve a series of steps such as reading, cleaning, summarizing and plotting data, statistical analysis and reporting…”
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Trimmed Constrained Mixed Effects Models: Formulations and Algorithms by Zheng, Peng, Barber, Ryan, Sorensen, Reed J. D., Murray, Christopher J. L., Aravkin, Aleksandr Y.

“…Mixed effects (ME) models inform a vast array of problems in the physical and social sciences, and are pervasive in meta-analysis…”
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Efficient implementation of the continuous-time hybridization expansion quantum impurity solver by Hafermann, Hartmut, Werner, Philipp, Gull, Emanuel

“…Strongly correlated quantum impurity problems appear in a wide variety of contexts ranging from nanoscience and surface physics to material science and the…”
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Manifold Markov chain Monte Carlo methods for Bayesian inference in diffusion models by Graham, Matthew M., Thiery, Alexandre H., Beskos, Alexandros

“…Bayesian inference for nonlinear diffusions, observed at discrete times, is a challenging task that has prompted the development of a number of algorithms,…”
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A Review of Adversarial Attack and Defense for Classification Methods by Li, Yao, Cheng, Minhao, Hsieh, Cho-Jui, Lee, Thomas C. M.

“…Despite the efficiency and scalability of machine learning systems, recent studies have demonstrated that many classification methods, especially Deep Neural…”
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False Discovery Rate Smoothing by Tansey, Wesley, Koyejo, Oluwasanmi, Poldrack, Russell A., Scott, James G.

“…We present false discovery rate (FDR) smoothing, an empirical-Bayes method for exploiting spatial structure in large multiple-testing problems. FDR smoothing…”
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Missing Value Imputation in Relational Data Using Variational Inference by Fontaine, Simon, Kang, Jian, Zhu, Ji

“…In real-world networks, node attributes are often only partially observed, necessitating imputation to support analysis or enable downstream tasks…”
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Percolation theory using Python by Malthe-Sørenssen, Anders

“… Readers will learn how to generate, analyze, and comprehend data and models, with detailed theoretical discussions complemented by accessible computer codes…”
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Prediction of Positive Patient Health Questionnaire-2 Screening Using Area Deprivation Index in Primary Care by Duarte, Martha, Salamanca, Mayra, Gonzalez, Juan M, Roman Laporte, Roberto, Gattamorta, Karina, Lopez Martinez, Fernando Enrique, Clochesy, John, Rincon Acuna, Juan Carlos

“…Depression is recognized as a significant public health issue in the United States. The National Survey on Drug Use and Health reports that 21.0 million adults…”
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Manifold lifting: scaling Markov chain Monte Carlo to the vanishing noise regime by Au, Khai Xiang, Graham, Matthew M, Thiery, Alexandre H

“…Standard Markov chain Monte Carlo methods struggle to explore distributions that concentrate in the neighbourhood of low-dimensional submanifolds. This…”
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Black Box Variational Bayesian Model Averaging by Kejzlar, Vojtech, Bhattacharya, Shrijita, Son, Mookyong, Maiti, Tapabrata

“…For many decades now, Bayesian Model Averaging (BMA) has been a popular framework to systematically account for model uncertainty that arises in situations…”
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Estimating Local Prevalence of Obesity Via Survey Under Cost Constraints: Stratifying ZCTAs in Virginia's Thomas Jefferson Health District by Lobo, Benjamin J., Bonds, Denise E., Kafadar, Karen

“… (here, ZIP Code Tabulation Areas, or ZCTAs) prior to conducting the survey for those situations where cost considerations make it infeasible to sample each geographic unit (here, ZCTA) in the region (here, TJHD…”
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Domain-specific decision modelling and statistical analysis for combat system effectiveness simulation by Li, Xiaobo, Lei, Yonglin, Vangheluwe, Hans, Wang, Weiping, Li, Qun

“… decision models to Python code which is supported by a Python script framework to implement decision models and we present a Bayesian network-based statistical analysis method on simulation output data…”
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