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To facilitate flexible and efficient structural bioinformatics analyses, new functionality for three-dimensional structure processing and analysis has been introduced into PyCogent -- a popular feature-rich framework for sequence-based…

Biomolecules · Quantitative Biology 2018-10-01 Marcin Cieslik , Zygmunt Derewenda , Cameron Mura

Consider a researcher estimating the parameters of a regression function based on data for all 50 states in the United States or on data for all visits to a website. What is the interpretation of the estimated parameters and the standard…

Statistics Theory · Mathematics 2019-06-25 Alberto Abadie , Susan Athey , Guido W. Imbens , Jeffrey M. Wooldridge

Dynamical systems theory has long provided a foundation for understanding evolving phenomena across scientific domains. Yet, the application of this theory to complex real-world systems remains challenging due to issues in mathematical…

Machine Learning · Computer Science 2024-11-05 Samuel A. Moore , Brian P. Mann , Boyuan Chen

We propose a procedural fruit tree rendering framework, based on Blender and Python scripts allowing to generate quickly labeled dataset (i.e. including ground truth semantic segmentation). It is designed to train image analysis deep…

Computer Vision and Pattern Recognition · Computer Science 2019-07-11 Thomas Duboudin , Maxime Petit , Liming Chen

The paper focuses on sequential experiments for categorical responses in which whether or not a further observation is made depends on the outcome of a previous experiment. Examples include subsequent medical interventions being performed…

Methodology · Statistics 2025-07-04 Anna Klimova , Tamás Rudas

Experimental design has emerged as a powerful approach for improving the sample efficiency of A/B testing, yet existing designs rely critically on correctly specified models. We study robust sequential experimental design under model…

Machine Learning · Statistics 2026-05-14 Qianglin Wen , Xiangkun Wu , Chengchun Shi , Ting Li , Niansheng Tang , Yingying Zhang , Hongtu Zhu

This paper considers the problem of design-based inference for the average treatment effect in finely stratified experiments. Here, by "design-based'' we mean that the only source of uncertainty stems from the randomness in treatment…

Econometrics · Economics 2025-05-08 Yuehao Bai , Xun Huang , Joseph P. Romano , Azeem M. Shaikh , Max Tabord-Meehan

A stepped wedge design is a unidirectional crossover design where clusters are randomized to distinct treatment sequences. While model-based analysis of stepped wedge designs is standard practice to evaluate treatment effects accounting for…

Methodology · Statistics 2024-09-13 Bingkai Wang , Xueqi Wang , Fan Li

The design of an experiment can be always be considered at least implicitly Bayesian, with prior knowledge used informally to aid decisions such as the variables to be studied and the choice of a plausible relationship between the…

Methodology · Statistics 2017-01-03 David C. Woods , Antony M. Overstall , Maria Adamou , Timothy W. Waite

Classical approaches to experimental design assume that intervening on one unit does not affect other units. There are many important settings, however, where this non-interference assumption does not hold, as when running experiments on…

Optimization and Control · Mathematics 2020-07-01 Stefan Wager , Kuang Xu

There are two main objectives of this paper. The first is to present a statistical framework for models with context specific independence structures, i.e., conditional independences holding only for sepcific values of the conditioning…

Artificial Intelligence · Computer Science 2013-01-18 Soren Hojsgaard

Numerical stability is a crucial requirement of reliable scientific computing. However, despite the pervasiveness of Python in data science, analyzing large Python programs remains challenging due to the lack of scalable numerical analysis…

Mathematical Software · Computer Science 2024-10-28 Yohan Chatelain , Nigel Yong , Gregory Kiar , Tristan Glatard

The optimal selection of experimental conditions is essential to maximizing the value of data for inference and prediction, particularly in situations where experiments are time-consuming and expensive to conduct. We propose a general…

Machine Learning · Statistics 2012-12-04 Xun Huan , Youssef M. Marzouk

Combining machine learning with econometric analysis is becoming increasingly prevalent in both research and practice. A common empirical strategy involves the application of predictive modeling techniques to 'mine' variables of interest…

Econometrics · Economics 2020-12-22 Mochen Yang , Edward McFowland , Gordon Burtch , Gediminas Adomavicius

All scientific interpretations of statistical outputs depend on background (auxiliary) assumptions that are rarely delineated or explicitly interrogated. These include not only the usual modeling assumptions, but also deeper assumptions…

Methodology · Statistics 2022-08-01 Sander Greenland , Zad Rafi , Robert Matthews , Megan Higgs

`scores` is a Python package containing mathematical functions for the verification, evaluation and optimisation of forecasts, predictions or models. It supports labelled n-dimensional (multidimensional) data, which is used in many…

Factorial designs are frequently used in different fields of science, e.g. psychological, medical or biometric studies. Standard approaches, as the ANOVA $F$-test, make different assumptions on the distribution of the error terms, the…

Methodology · Statistics 2018-02-21 Maria Umlauft

In this review, we present econometric and statistical methods for analyzing randomized experiments. For basic experiments we stress randomization-based inference as opposed to sampling-based inference. In randomization-based inference,…

Methodology · Statistics 2017-10-26 Susan Athey , Guido Imbens

Bipartite experiments arise in various fields, in which the treatments are randomized over one set of units, while the outcomes are measured over another separate set of units. However, existing methods often rely on strong model…

Methodology · Statistics 2025-04-16 Sizhu Lu , Lei Shi , Yue Fang , Wenxin Zhang , Peng Ding

Ground truth labels/outcomes are critical for advancing scientific and engineering applications, e.g., evaluating the treatment effect of an intervention or performance of a predictive model. Since randomly sampling inputs for labeling can…

Machine Learning · Computer Science 2025-02-11 Daksh Mittal , Yuanzhe Ma , Shalmali Joshi , Hongseok Namkoong