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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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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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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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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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Statistics Using Python by Campesato, Oswald

“…This book is designed to offer a fast-paced yet thorough introduction to essential statistical concepts using Python code samples, and aims to assist data scientists in their daily endeavors…”
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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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Generation of Scale-Free Assortative Networks via Newman Rewiring for Simulation of Diffusion Phenomena by Di Lucchio, Laura, Modanese, Giovanni

“…By collecting and expanding several numerical recipes developed in previous work, we implement an object-oriented Python code, based on the networkX library, for the realization of the configuration…”
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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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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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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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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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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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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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Much Ado About Survey Tables: A Comparison of Chi-Square Tests and Software to Analyze Categorical Survey Data by Hu, Li-Yen R., He, Yulei, Irimata, Katherine E., Beresovsky, Vladislav

“… This article aims to fill such a gap. Many modern statistical software packages for survey analysis are capable of computing either the Wald Chi-square test or the Rao…”
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Machine learning with physically grounded, interpretable descriptors for polymer property prediction and monomer design by Averochkin, Gleb, Zlobin, Ivan, Bespalov, Ivan, Alexandrov, Eugeny

“…: VdW volumes, fragment counts, bonding stats, RDKit, xTB.•GPR models predict density, Tg, Tm and Td of homopolymers from monomer structures…”
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Robust distributed precision matrix estimation for high-dimensional data by Ye, Yangqing, Yu, Yang, Ma, Xiaoyan, Liang, Wanfeng

“… Simulation studies and real data analysis demonstrate the superiority of the proposed method. The complete Python code supporting this study can be downloaded from https://github.com/littletesla/RDPM …”
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Graph analysis and visualization: discovering business opportunity in linked data by Brath, Richard, Jonker, David

“… The companion website offers data sets, full code examples in Python, and links to all the tools covered in the book…”
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NODESTUDIO, A VISUAL PROGRAMMING FRAMEWORK FOR MUSCULOSKELETAL MRI ANALYSIS by Mendoza, M.A., Huo, Z., Diao, Y., Jin, Y., Huang, J., Bangerter, N.K.

“… to either implement or integrate software repositories in a clinical researcher's analysis pipeline…”
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Spatial Analysis Using Big Data by Hajime Seya, Yoshiki Yamagata

“…Spatial Analysis Using Big Data: Methods and Urban Applications helps readers understand the most powerful, state-of-the-art spatial econometric methods, focusing particularly on urban research problems…”
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