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Machine learning solutions are very popular in the field of chemoinformatics, where they have numerous applications, such as novel drug discovery or molecular property prediction. Molecular fingerprints are algorithms commonly used for…

Quantitative Methods · Quantitative Biology 2024-04-01 Michał Szafarczyk , Piotr Ludynia , Przemysław Kukla

mlpack is an open-source C++ machine learning library with an emphasis on speed and flexibility. Since its original inception in 2007, it has grown to be a large project implementing a wide variety of machine learning algorithms, from…

Mathematical Software · Computer Science 2017-08-31 Ryan R. Curtin , Marcus Edel

Robust machine learning is an increasingly important topic that focuses on developing models resilient to various forms of imperfect data. Due to the pervasiveness of recommender systems in online technologies, researchers have carried out…

Information Retrieval · Computer Science 2022-01-13 Zohreh Ovaisi , Shelby Heinecke , Jia Li , Yongfeng Zhang , Elena Zheleva , Caiming Xiong

We introduce Invariant Risk Minimization (IRM), a learning paradigm to estimate invariant correlations across multiple training distributions. To achieve this goal, IRM learns a data representation such that the optimal classifier, on top…

Machine Learning · Statistics 2020-03-31 Martin Arjovsky , Léon Bottou , Ishaan Gulrajani , David Lopez-Paz

ABCpy is a highly modular scientific library for Approximate Bayesian Computation (ABC) written in Python. The main contribution of this paper is to document a software engineering effort that enables domain scientists to easily apply ABC…

With the recent rapid progress in the study of deep generative models (DGMs), there is a need for a framework that can implement them in a simple and generic way. In this research, we focus on two features of DGMs: (1) deep neural networks…

Machine Learning · Computer Science 2023-09-25 Masahiro Suzuki , Takaaki Kaneko , Yutaka Matsuo

We study conditional risk minimization (CRM), i.e. the problem of learning a hypothesis of minimal risk for prediction at the next step of sequentially arriving dependent data. Despite it being a fundamental problem, successful learning in…

Machine Learning · Statistics 2018-11-06 Alexander Zimin , Christoph Lampert

We introduce PrivPy, a practical privacy-preserving collaborative computation framework, especially optimized for machine learning tasks. PrivPy provides an easy-to-use and highly compatible Python programming front-end which supports…

Cryptography and Security · Computer Science 2020-04-22 Yi Li , Yitao Duan , Yu Yu , Shuoyao Zhao , Wei Xu

In this work, we present scikit-fingerprints, a Python package for computation of molecular fingerprints for applications in chemoinformatics. Our library offers an industry-standard scikit-learn interface, allowing intuitive usage and easy…

Software Engineering · Computer Science 2025-08-12 Jakub Adamczyk , Piotr Ludynia

Most methods for learning with noisy labels require privileged knowledge such as noise transition matrices, clean subsets or pretrained feature extractors, resources typically unavailable when robustness is most needed. We propose Conformal…

Machine Learning · Computer Science 2026-04-13 Yuanjie Shi , Peihong Li , Zijian Zhang , Janardhan Rao Doppa , Yan Yan

HiClass is an open-source Python library for local hierarchical classification entirely compatible with scikit-learn. It contains implementations of the most common design patterns for hierarchical machine learning models found in the…

Machine Learning · Computer Science 2023-01-24 Fábio M. Miranda , Niklas Köhnecke , Bernhard Y. Renard

We consider robust empirical risk minimization (ERM), where model parameters are chosen to minimize the worst-case empirical loss when each data point varies over a given convex uncertainty set. In some simple cases, such problems can be…

Optimization and Control · Mathematics 2024-09-17 Eric Luxenberg , Dhruv Malik , Yuanzhi Li , Aarti Singh , Stephen Boyd

Risk-sensitive reinforcement learning (RL) has become a popular tool for controlling the risk of uncertain outcomes and ensuring reliable performance in highly stochastic sequential decision-making problems. While it has been shown that…

Machine Learning · Computer Science 2026-01-21 Xian Yu , Lei Ying

This paper targets the efficient construction of a safety shield for decision making in scenarios that incorporate uncertainty. Markov decision processes (MDPs) are prominent models to capture such planning problems. Reinforcement learning…

Artificial Intelligence · Computer Science 2019-11-26 Nils Jansen , Bettina Könighofer , Sebastian Junges , Alexandru C. Serban , Roderick Bloem

Short Read Alignment Mapping Metrics (SRAMM): is an efficient and versatile command line tool providing additional short read mapping metrics, filtering, and graphs. Short read aligners report MAPing Quality (MAPQ), but these methods…

Genomics · Quantitative Biology 2021-07-08 Alvin Chon , Xiaoqiu Huang

Robust estimation provides essential tools for analyzing data that contain outliers, ensuring that statistical models remain reliable even in the presence of some anomalous data. While robust methods have long been available in R, users of…

Computation · Statistics 2024-11-05 Sarah Leyder , Jakob Raymaekers , Peter J. Rousseeuw , Thomas Servotte , Tim Verdonck

MushroomRL is an open-source Python library developed to simplify the process of implementing and running Reinforcement Learning (RL) experiments. Compared to other available libraries, MushroomRL has been created with the purpose of…

Machine Learning · Computer Science 2020-01-10 Carlo D'Eramo , Davide Tateo , Andrea Bonarini , Marcello Restelli , Jan Peters

The statistical characteristics of instance-label pairs often change with time in practical scenarios of supervised classification. Conventional learning techniques adapt to such concept drift accounting for a scalar rate of change by means…

Machine Learning · Statistics 2022-06-01 Verónica Álvarez , Santiago Mazuelas , Jose A. Lozano

We introduce GraSPy, a Python library devoted to statistical inference, machine learning, and visualization of random graphs and graph populations. This package provides flexible and easy-to-use algorithms for analyzing and understanding…

Social and Information Networks · Computer Science 2019-10-25 Jaewon Chung , Benjamin D. Pedigo , Eric W. Bridgeford , Bijan K. Varjavand , Hayden S. Helm , Joshua T. Vogelstein

We present $\textbf{PyRMLE}$, a Python module that implements Regularized Maximum Likelihood Estimation for the analysis of Random Coefficient models. $\textbf{PyRMLE}$ is simple to use and readily works with data formats that are typical…

Computation · Statistics 2021-08-17 Emil Mendoza , Fabian Dunker , Marco Reale