TorchCP: A Python Library for Conformal Prediction
Southern University of Science and Technology（南方科技大学）；Nanyang Technological University（南洋理工大学）；Nanjing University（南京大学）；The Chinese University of Hong Kong, Shenzhen（香港中文大学（深圳））
Conformal prediction (CP) is a powerful statistical framework that generates prediction intervals or sets with guaranteed coverage probability. While CP algorithms have evolved beyond traditional classifiers and regressors to sophisticated deep learning models like deep neural networks (DNNs), graph neural networks (GNNs), and large language models (LLMs), existing CP libraries often lack the model support and scalability for large-scale deep learning (DL) scenarios. This paper introduces TorchCP, a PyTorch-native library designed to integrate state-of-the-art CP algorithms into DL techniques, including DNN-based classifiers/regressors, GNNs, and LLMs. Released under the LGPL-3.0 license, TorchCP comprises about 16k lines of code, validated with 100\% unit test coverage and detailed documentation. Notably, TorchCP enables CP-specific training algorithms, online prediction, and GPU-accelerated batch processing, achieving up to 90\% reduction in inference time on large datasets. With its low-coupling design, comprehensive suite of advanced methods, and full GPU scalability, TorchCP empowers researchers and practitioners to enhance uncertainty quantification across cutting-edge applications.
This paper introduces libconform v0.1.0, a Python library for the conformal prediction framework, licensed under the MIT-license. libconform is not yet stable. This paper describes the main algorithms implemented and documents the API of libconform. Also some details about the implementation and changes in future versions are described.
University of California-Irvine（加州大学欧文分校）；Siemens Corporate Technology（西门子企业技术公司）；University of Southern California（南加州大学）
Pykg2vec is an open-source Python library for learning the representations of the entities and relations in knowledge graphs. Pykg2vec's flexible and modular software architecture currently implements 16 state-of-the-art knowledge graph embedding algorithms, and is designed to easily incorporate new algorithms. The goal of pykg2vec is to provide a practical and educational platform to accelerate research in knowledge graph representation learning. Pykg2vec is built on top of TensorFlow and Python's multiprocessing framework and provides modules for batch generation, Bayesian hyperparameter opt…
The University of Edinburgh（爱丁堡大学）；Central European University（中欧大学）
Sampling graphs is an important task in data mining. In this paper, we describe Little Ball of Fur a Python library that includes more than twenty graph sampling algorithms. Our goal is to make node, edge, and exploration-based network sampling techniques accessible to a large number of professionals, researchers, and students in a single streamlined framework. We created this framework with a focus on a coherent application public interface which has a convenient design, generic input data requirements, and reasonable baseline settings of algorithms. Here we overview these design foundations …
Google Research（谷歌研究院）；Carnegie Mellon University（卡内基梅隆大学）
Graph representations of programs are commonly a central element of machine learning for code research. We introduce an open source Python library python_graphs that applies static analysis to construct graph representations of Python programs suitable for training machine learning models. Our library admits the construction of control-flow graphs, data-flow graphs, and composite ``program graphs'' that combine control-flow, data-flow, syntactic, and lexical information about a program. We present the capabilities and limitations of the library, perform a case study applying the library to mil…
We present srlearn, a Python library for boosted statistical relational models. We adapt the scikit-learn interface to this setting and provide examples for how this can be used to express learning and inference problems.
Rotman Research Institute（罗特曼研究所）；Baycrest Health Sciences（贝里克雷斯健康科学中心）
Kernel methods have proven to be powerful techniques for pattern analysis and machine learning (ML) in a variety of domains. However, many of their original or advanced implementations remain in Matlab. With the incredible rise and adoption of Python in the ML and data science world, there is a clear need for a well-defined library that enables not only the use of popular kernels, but also allows easy definition of customized kernels to fine-tune them for diverse applications. The kernelmethods library fills that important void in the python ML ecosystem in a domain-agnostic fashion, allowing …
NIMFA is an open-source Python library that provides a unified interface to nonnegative matrix factorization algorithms. It includes implementations of state-of-the-art factorization methods, initialization approaches, and quality scoring. It supports both dense and sparse matrix representation. NIMFA's component-based implementation and hierarchical design should help the users to employ already implemented techniques or design and code new strategies for matrix factorization tasks.
University of Edinburgh（爱丁堡大学）；Eindhoven University of Technology（埃因霍温理工大学）
DeeProb-kit is a unified library written in Python consisting of a collection of deep probabilistic models (DPMs) that are tractable and exact representations for the modelled probability distributions. The availability of a representative selection of DPMs in a single library makes it possible to combine them in a straightforward manner, a common practice in deep learning research nowadays. In addition, it includes efficiently implemented learning techniques, inference routines, statistical algorithms, and provides high-quality fully-documented APIs. The development of DeeProb-kit will help t…
This paper introduces PyGAD, an open-source easy-to-use Python library for building the genetic algorithm. PyGAD supports a wide range of parameters to give the user control over everything in its life cycle. This includes, but is not limited to, population, gene value range, gene data type, parent selection, crossover, and mutation. PyGAD is designed as a general-purpose optimization library that allows the user to customize the fitness function. Its usage consists of 3 main steps: build the fitness function, create an instance of the pygad.GA class, and calling the pygad.GA.run() method. The…
Organizations have realized the importance of data analysis and its benefits. This in combination with Machine Learning algorithms has allowed to solve problems more easily, making these processes less time-consuming. Neural networks are the Machine Learning technique that is recently obtaining very good best results. This paper describes an open-source Python library called GEMA developed to work with a type of neural network model called Self-Organizing-Maps. GEMA is freely available under GNU General Public License at GitHub (https://github.com/ufvceiec/GEMA). The library has been evaluated…
University of Cambridge（剑桥大学）；Universita’ di Siena（锡耶纳大学）
"PyTorch, Explain!" is a Python module integrating a variety of state-of-the-art approaches to provide logic explanations from neural networks. This package focuses on bringing these methods to non-specialists. It has minimal dependencies and it is distributed under the Apache 2.0 licence allowing both academic and commercial use. Source code and documentation can be downloaded from the github repository: https://github.com/pietrobarbiero/pytorch_explain.
We describe a new library named picasso, which implements a unified framework of pathwise coordinate optimization for a variety of sparse learning problems (e.g., sparse linear regression, sparse logistic regression, sparse Poisson regression and scaled sparse linear regression) combined with efficient active set selection strategies. Besides, the library allows users to choose different sparsity-inducing regularizers, including the convex $\ell_1$, nonconvex MCP and SCAD regularizers. The library is coded in C++ and has user-friendly R and Python wrappers. Numerical experiments demonstrate th…
Wrocław University of Science and Technology（弗罗茨瓦夫科技大学）
stream-learn is a Python package compatible with scikit-learn and developed for the drifting and imbalanced data stream analysis. Its main component is a stream generator, which allows to produce a synthetic data stream that may incorporate each of the three main concept drift types (i.e. sudden, gradual and incremental drift) in their recurring or non-recurring versions. The package allows conducting experiments following established evaluation methodologies (i.e. Test-Then-Train and Prequential). In addition, estimators adapted for data stream classification have been implemented, including …
Laboratoire d’imagerie, vision et intelligence artificielle (LIVIA)（图像、视觉与人工智能实验室（LIVIA））；École de Technologie Supérieure (ÉTS) - Université du Québec（魁北克大学高等技术学院（ÉTS））；Centro de Informática - Universidade Federal de Pernambuco（伯南布哥联邦大学信息中心）
DESlib is an open-source python library providing the implementation of several dynamic selection techniques. The library is divided into three modules: (i) \emph{dcs}, containing the implementation of dynamic classifier selection methods (DCS); (ii) \emph{des}, containing the implementation of dynamic ensemble selection methods (DES); (iii) \emph{static}, with the implementation of static ensemble techniques. The library is fully documented (documentation available online on Read the Docs), has a high test coverage (codecov.io) and is part of the scikit-learn-contrib supported projects. Docum…
Meta-learning (a.k.a. learning to learn) has recently emerged as a promising paradigm for a variety of applications. There are now many meta-learning methods, each focusing on different modeling aspects of base and meta learners, but all can be (re)formulated as specific bilevel optimization problems. This work presents BOML, a modularized optimization library that unifies several meta-learning algorithms into a common bilevel optimization framework. It provides a hierarchical optimization pipeline together with a variety of iteration modules, which can be used to solve the mainstream categori…
Technische Universität Berlin（柏林工业大学）；BASF SE（巴斯夫欧洲公司）
This paper describes the autofeat Python library, which provides scikit-learn style linear regression and classification models with automated feature engineering and selection capabilities. Complex non-linear machine learning models, such as neural networks, are in practice often difficult to train and even harder to explain to non-statisticians, who require transparent analysis results as a basis for important business decisions. While linear models are efficient and intuitive, they generally provide lower prediction accuracies. Our library provides a multi-step feature engineering and selec…
Universidad de Zaragoza（萨拉戈萨大学）；Hiberus（Hiberus公司）
This paper presents a new Python library for anomaly detection in unsupervised learning approaches. The input for the library is a univariate time series representing observations of a given phenomenon. Then, it can identify anomalous epochs, i.e., time intervals where the observations are above a given percentile of a baseline distribution, defined by a dissimilarity metric. Using time-evolving graphs for the anomaly detection, the library leverages valuable information given by the inter-dependencies among data. Currently, the library implements 28 different dissimilarity metrics, and it has…
UPMC Université Paris 6, Sorbonne Universités（巴黎第六大学（UPMC），索邦大学集团）；École Polytechnique（巴黎综合理工学院）；Athens University of Economics and Business（雅典经济与商业大学）
The problem of accurately measuring the similarity between graphs is at the core of many applications in a variety of disciplines. Graph kernels have recently emerged as a promising approach to this problem. There are now many kernels, each focusing on different structural aspects of graphs. Here, we present GraKeL, a library that unifies several graph kernels into a common framework. The library is written in Python and adheres to the scikit-learn interface. It is simple to use and can be naturally combined with scikit-learn's modules to build a complete machine learning pipeline for tasks su…
Rochester Institute of Technology（罗切斯特理工学院）；IBM T. J. Watson Research Center（IBM托马斯·J·沃森研究中心）
Open Cyber threat intelligence (OpenCTI) information is available in an unstructured format from heterogeneous sources on the Internet. We present CyNER, an open-source python library for cybersecurity named entity recognition (NER). CyNER combines transformer-based models for extracting cybersecurity-related entities, heuristics for extracting different indicators of compromise, and publicly available NER models for generic entity types. We provide models trained on a diverse corpus that users can readily use. Events are described as classes in previous research - MALOnt2.0 (Christian et al.,…
Wax is what you put on a surfboard to avoid slipping. It is an essential tool to go surfing... We introduce WAX-ML a research-oriented Python library providing tools to design powerful machine learning algorithms and feedback loops working on streaming data. It strives to complement JAX with tools dedicated to time series. WAX-ML makes JAX-based programs easy to use for end-users working with pandas and xarray for data manipulation. It provides a simple mechanism for implementing feedback loops, allows the implementation of online learning and reinforcement learning algorithms with functions, …
Southern University of Science and Technology（南方科技大学）；Peng Cheng Laboratory（鹏城实验室）
This paper presents LibMTL, an open-source Python library built on PyTorch, which provides a unified, comprehensive, reproducible, and extensible implementation framework for Multi-Task Learning (MTL). LibMTL considers different settings and approaches in MTL, and it supports a large number of state-of-the-art MTL methods, including 12 loss weighting strategies, 7 architectures, and 84 combinations of different architectures and loss weighting methods. Moreover, the modular design in LibMTL makes it easy-to-use and well extensible, thus users can easily and fast develop new MTL methods, compar…
In this paper, we present a new Python library called mPyPl, which is intended to simplify complex data processing tasks using functional approach. This library defines operations on lazy data streams of named dictionaries represented as generators (so-called multi-field datastreams), and allows enriching those data streams with more 'fields' in the process of data preparation and feature extraction. Thus, most data preparation tasks can be expressed in the form of neat linear 'pipeline', similar in syntax to UNIX pipes, or |> functional composition operator in F#. We define basic operations o…
We introduce a Python open-source library for $\mathcal{X}$-armed bandit and online blackbox optimization named PyXAB. PyXAB contains the implementations for more than 10 $\mathcal{X}$-armed bandit algorithms, such as HOO, StoSOO, HCT, and the most recent works GPO and VHCT. PyXAB also provides the most commonly-used synthetic objectives to evaluate the performance of different algorithms and the various choices of the hierarchical partitions on the parameter space. The online documentation for PyXAB includes clear instructions for installation, straight-forward examples, detailed feature desc…
Synthetic data is widely used in various domains. This is because many modern algorithms require lots of data for efficient training, and data collection and labeling usually are a time-consuming process and are prone to errors. Furthermore, some real-world data, due to its nature, is confidential and cannot be shared. Bayesian networks are a type of probabilistic graphical model widely used to model the uncertainties in real-world processes. Dynamic Bayesian networks are a special class of Bayesian networks that model temporal and time series data. In this paper, we introduce the tsBNgen, a P…
Tuning hyperparameters for machine learning algorithms is a tedious task, one that is typically done manually. To enable automated hyperparameter tuning, recent works have started to use techniques based on Bayesian optimization. However, to practically enable automated tuning for large scale machine learning training pipelines, significant gaps remain in existing libraries, including lack of abstractions, fault tolerance, and flexibility to support scheduling on any distributed computing framework. To address these challenges, we present Mango, a Python library for parallel hyperparameter tun…
Hasso Plattner Institute（哈索·普拉特纳研究院）；University of Potsdam（波茨坦大学）；Free University of Berlin（柏林自由大学）
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 literature, that is, the local classifiers per node, per parent node and per level. Additionally, the package contains implementations of hierarchical metrics, which are more appropriate for evaluating classification performance on hierarchical data. The documentation includes installation and usage instructions, examples within tutorials and interactive notebook…
abess: A Fast Best Subset Selection Library in Python and R
Sun Yat-Sen University（中山大学）；University of Science and Technology of China（中国科学技术大学）；Renmin University of China（中国人民大学）；Peking University（北京大学）；National University of Singapore（新加坡国立大学）
Wrocław University of Science and Technology（弗罗茨瓦夫理工大学）；illimites foundation（伊利米特斯基金会）
scikit-multilearn is a Python library for performing multi-label classification. The library is compatible with the scikit/scipy ecosystem and uses sparse matrices for all internal operations. It provides native Python implementations of popular multi-label classification methods alongside a novel framework for label space partitioning and division. It includes modern algorithm adaptation methods, network-based label space division approaches, which extracts label dependency information and multi-label embedding classifiers. It provides python wrapped access to the extensive multi-label method…
Wrocław University of Science and Technology（弗罗茨瓦夫理工大学）
The classification problem's complexity assessment is an essential element of many topics in the supervised learning domain. It plays a significant role in meta-learning -- becoming the basis for determining meta-attributes or multi-criteria optimization -- allowing the evaluation of the training set resampling without needing to rebuild the recognition model. The tools currently available for the academic community, which would enable the calculation of problem complexity measures, are available only as libraries of the C++ and R languages. This paper describes the software module that allows…
A large amount of data is produced every second from modern information systems such as mobile devices, the world wide web, Internet of Things, social media, etc. Analysis and mining of this massive data requires a lot of advanced tools and techniques. Therefore, big data analytics and mining is currently an active and trending area of research because of the enormous benefits businesses and organizations derive from it. Numerous tools like Pandas, Numpy, STATA, SPSS, have been created to help analyze and mine these huge outburst of data and some have become so popular and widely used in the f…
New York University（纽约大学）；Adobe Research（奥多比研究院）；Universitat Pompeu Fabra（庞培法布拉大学）
Soundata is a Python library for loading and working with audio datasets in a standardized way, removing the need for writing custom loaders in every project, and improving reproducibility by providing tools to validate data against a canonical version. It speeds up research pipelines by allowing users to quickly download a dataset, load it into memory in a standardized and reproducible way, validate that the dataset is complete and correct, and more. Soundata is based and inspired on mirdata and design to complement mirdata by working with environmental sound, bioacoustic and speech datasets,…
We introduce the TimeGym Forecasting Debugging Toolkit, a Python library for testing and debugging time series forecasting pipelines. TimeGym simplifies the testing forecasting pipeline by providing generic tests for forecasting pipelines fresh out of the box. These tests are based on common modeling challenges of time series. Our library enables forecasters to apply a Test-Driven Development approach to forecast modeling, using specified oracles to generate artificial data with noise.
We present \texttt{secml}, an open-source Python library for secure and explainable machine learning. It implements the most popular attacks against machine learning, including test-time evasion attacks to generate adversarial examples against deep neural networks and training-time poisoning attacks against support vector machines and many other algorithms. These attacks enable evaluating the security of learning algorithms and the corresponding defenses under both white-box and black-box threat models. To this end, \texttt{secml} provides built-in functions to compute security evaluation curv…
Department of Signal Theory and Communications, Universidad Carlos III de Madrid（马德里卡洛斯三世大学信号理论与通信系）
We introduce PyHHMM, an object-oriented open-source Python implementation of Heterogeneous-Hidden Markov Models (HHMMs). In addition to HMM's basic core functionalities, such as different initialization algorithms and classical observations models, i.e., continuous and multinoulli, PyHHMM distinctively emphasizes features not supported in similar available frameworks: a heterogeneous observation model, missing data inference, different model order selection criterias, and semi-supervised training. These characteristics result in a feature-rich implementation for researchers working with sequen…
School of Computer Science and Informatics（计算机科学与信息学院）；Cardiff University（卡迪夫大学）
Language model (LM) pretraining has led to consistent improvements in many NLP downstream tasks, including named entity recognition (NER). In this paper, we present T-NER (Transformer-based Named Entity Recognition), a Python library for NER LM finetuning. In addition to its practical utility, T-NER facilitates the study and investigation of the cross-domain and cross-lingual generalization ability of LMs finetuned on NER. Our library also provides a web app where users can get model predictions interactively for arbitrary text, which facilitates qualitative model evaluation for non-expert pro…
seqme: a Python library for evaluating biological sequence design
Institute of AI for Health, Helmholtz Munich（亥姆霍兹慕尼黑人工智能健康研究所）；Technical University of Munich（慕尼黑工业大学）；University of Warsaw（华沙大学）；Warsaw University of Technology（华沙理工大学）
University of Sussex（萨塞克斯大学）；Singapore University of Technology and Design（新加坡科技设计大学）
We present a Python library, called Midi Miner, that can calculate tonal tension and classify different tracks. MIDI (Music Instrument Digital Interface) is a hardware and software standard for communicating musical events between digital music devices. It is often used for tasks such as music representation, communication between devices, and even music generation [5]. Tension is an essential element of the music listening experience, which can come from a number of musical features including timbre, loudness and harmony [3]. Midi Miner provides a Python implementation for the tonal tension m…
Multiple Kernel Learning is a recent and powerful paradigm to learn the kernel function from data. In this paper, we introduce MKLpy, a python-based framework for Multiple Kernel Learning. The library provides Multiple Kernel Learning algorithms for classification tasks, mechanisms to compute kernel functions for different data types, and evaluation strategies. The library is meant to maximize the usability and to simplify the development of novel solutions.
Digital hardware is verified by comparing its behavior against a reference model on a range of randomly generated input signals. The random generation of the inputs hopes to achieve sufficient coverage of the different parts of the design. However, such coverage is often difficult to achieve, amounting to large verification efforts and delays. An alternative is to use Reinforcement Learning (RL) to generate the inputs by learning to prioritize those inputs which can more efficiently explore the design under test. In this work, we present VeRLPy an open-source library to allow RL-driven verific…
