Daily Papers

Ensuring the security and reliability of machine learning frameworks is crucial for building trustworthy AI-based systems. Fuzzing, a popular technique in secure software development lifecycle (SSDLC), can be used to develop secure and robust software. Popular machine learning frameworks such as PyTorch and TensorFlow are complex and written in multiple programming languages including C/C++ and Python. We propose a dynamic analysis pipeline for Python projects using the Sydr-Fuzz toolset. Our pipeline includes fuzzing, corpus minimization, crash triaging, and coverage collection. Crash triaging and severity estimation are important steps to ensure that the most critical vulnerabilities are addressed promptly. Furthermore, the proposed pipeline is integrated in GitLab CI. To identify the most vulnerable parts of the machine learning frameworks, we analyze their potential attack surfaces and develop fuzz targets for PyTorch, TensorFlow, and related projects such as h5py. Applying our dynamic analysis pipeline to these targets, we were able to discover 3 new bugs and propose fixes for them.

Python is one of the fastest-growing programming languages and currently ranks as the top language in many lists, even recently overtaking JavaScript as the top language on GitHub. Given its importance in data science and machine learning, it is imperative to be able to effectively train LLMs to generate good unit test cases for Python code. This motivates the need for a large dataset to provide training and testing data. To date, while other large datasets exist for languages like Java, none publicly exist for Python. Python poses difficult challenges in generating such a dataset, due to its less rigid naming requirements. In this work, we consider two commonly used Python unit testing frameworks: Pytest and unittest. We analyze a large corpus of over 88K open-source GitHub projects utilizing these testing frameworks. Using a carefully designed set of heuristics, we are able to locate over 22 million test methods. We then analyze the test and non-test code and map individual unit tests to the focal method being tested. This provides an explicit traceability link from the test to the tested method. Our pyMethods2Test dataset contains over 2 million of these focal method mappings, as well as the ability to generate useful context for input to LLMs. The pyMethods2Test dataset is publicly available on Zenodo at: https://doi.org/10.5281/zenodo.14264518

Python type inference is challenging in practice. Due to its dynamic properties and extensive dependencies on third-party libraries without type annotations, the performance of traditional static analysis techniques is limited. Although semantics in source code can help manifest intended usage for variables (thus help infer types), they are usually ignored by existing tools. In this paper, we propose PYInfer, an end-to-end learning-based type inference tool that automatically generates type annotations for Python variables. The key insight is that contextual code semantics is critical in inferring the type for a variable. For each use of a variable, we collect a few tokens within its contextual scope, and design a neural network to predict its type. One challenge is that it is difficult to collect a high-quality human-labeled training dataset for this purpose. To address this issue, we apply an existing static analyzer to generate the ground truth for variables in source code. Our main contribution is a novel approach to statically infer variable types effectively and efficiently. Formulating the type inference as a classification problem, we can handle user-defined types and predict type probabilities for each variable. Our model achieves 91.2% accuracy on classifying 11 basic types in Python and 81.2% accuracy on classifying 500 most common types. Our results substantially outperform the state-of-the-art type annotators. Moreover, PYInfer achieves 5.2X more code coverage and is 187X faster than a state-of-the-art learning-based tool. With similar time consumption, our model annotates 5X more variables than a state-of-the-art static analysis tool. Our model also outperforms a learning-based function-level annotator on annotating types for variables and function arguments. All our tools and datasets are publicly available to facilitate future research in this direction.

We introduce ESPnet-EZ, an extension of the open-source speech processing toolkit ESPnet, aimed at quick and easy development of speech models. ESPnet-EZ focuses on two major aspects: (i) easy fine-tuning and inference of existing ESPnet models on various tasks and (ii) easy integration with popular deep neural network frameworks such as PyTorch-Lightning, Hugging Face transformers and datasets, and Lhotse. By replacing ESPnet design choices inherited from Kaldi with a Python-only, Bash-free interface, we dramatically reduce the effort required to build, debug, and use a new model. For example, to fine-tune a speech foundation model, ESPnet-EZ, compared to ESPnet, reduces the number of newly written code by 2.7x and the amount of dependent code by 6.7x while dramatically reducing the Bash script dependencies. The codebase of ESPnet-EZ is publicly available.

Answering visual queries is a complex task that requires both visual processing and reasoning. End-to-end models, the dominant approach for this task, do not explicitly differentiate between the two, limiting interpretability and generalization. Learning modular programs presents a promising alternative, but has proven challenging due to the difficulty of learning both the programs and modules simultaneously. We introduce ViperGPT, a framework that leverages code-generation models to compose vision-and-language models into subroutines to produce a result for any query. ViperGPT utilizes a provided API to access the available modules, and composes them by generating Python code that is later executed. This simple approach requires no further training, and achieves state-of-the-art results across various complex visual tasks.

In this paper, we present a pure-Python library called PyPop7 for black-box optimization (BBO). As population-based methods are becoming increasingly popular for BBO, our design goal is to provide a unified API and elegant implementations for them, particularly in high-dimensional cases. Since population-based methods suffer easily from the curse of dimensionality owing to their random sampling nature, various improvements have been proposed to alleviate this issue via exploiting possible problem structures: such as space decomposition, low-memory approximation, low-rank metric learning, variance reduction, ensemble of random subspaces, model self-adaptation, and smoothing. Now PyPop7 has covered these advances with >72 versions and variants of 13 BBO algorithm families from different research communities. Its open-source code and full-fledged documents are available at https://github.com/Evolutionary-Intelligence/pypop and https://pypop.readthedocs.io, respectively.

We present a new regular grid search algorithm for quick fixed-radius nearest-neighbor lookup developed in Python. This module indexes a set of k-dimensional points in a regular grid, with optional periodic conditions, providing a fast approach for nearest neighbors queries. In this first installment we provide three types of queries: bubble, shell and the nth-nearest; as well as three different metrics of interest in astronomy: the euclidean and two distance functions in spherical coordinates of varying precision, haversine and Vincenty; and the possibility of providing a custom distance function. This package results particularly useful for large datasets where a brute-force search turns impractical.

Theano is a Python library that allows to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently. Since its introduction, it has been one of the most used CPU and GPU mathematical compilers - especially in the machine learning community - and has shown steady performance improvements. Theano is being actively and continuously developed since 2008, multiple frameworks have been built on top of it and it has been used to produce many state-of-the-art machine learning models. The present article is structured as follows. Section I provides an overview of the Theano software and its community. Section II presents the principal features of Theano and how to use them, and compares them with other similar projects. Section III focuses on recently-introduced functionalities and improvements. Section IV compares the performance of Theano against Torch7 and TensorFlow on several machine learning models. Section V discusses current limitations of Theano and potential ways of improving it.

Scikit-learn is a Python module integrating a wide range of state-of-the-art machine learning algorithms for medium-scale supervised and unsupervised problems. This package focuses on bringing machine learning to non-specialists using a general-purpose high-level language. Emphasis is put on ease of use, performance, documentation, and API consistency. It has minimal dependencies and is distributed under the simplified BSD license, encouraging its use in both academic and commercial settings. Source code, binaries, and documentation can be downloaded from http://scikit-learn.org.

Retrieval, re-ranking, and retrieval-augmented generation (RAG) are critical components of modern applications in information retrieval, question answering, or knowledge-based text generation. However, existing solutions are often fragmented, lacking a unified framework that easily integrates these essential processes. The absence of a standardized implementation, coupled with the complexity of retrieval and re-ranking workflows, makes it challenging for researchers to compare and evaluate different approaches in a consistent environment. While existing toolkits such as Rerankers and RankLLM provide general-purpose reranking pipelines, they often lack the flexibility required for fine-grained experimentation and benchmarking. In response to these challenges, we introduce Rankify, a powerful and modular open-source toolkit designed to unify retrieval, re-ranking, and RAG within a cohesive framework. Rankify supports a wide range of retrieval techniques, including dense and sparse retrievers, while incorporating state-of-the-art re-ranking models to enhance retrieval quality. Additionally, Rankify includes a collection of pre-retrieved datasets to facilitate benchmarking, available at Huggingface (https://huggingface.co/datasets/abdoelsayed/reranking-datasets-light). To encourage adoption and ease of integration, we provide comprehensive documentation (http://rankify.readthedocs.io/), an open-source implementation on GitHub (https://github.com/DataScienceUIBK/rankify), and a PyPI package for easy installation (https://pypi.org/project/rankify/). As a unified and lightweight framework, Rankify allows researchers and practitioners to advance retrieval and re-ranking methodologies while ensuring consistency, scalability, and ease of use.

With the release of ever more capable large language models (LLMs), researchers in NLP and related disciplines have started to explore the usability of LLMs for a wide variety of different annotation tasks. Very recently, a lot of this attention has shifted to tasks that are subjective in nature. Given that the latest generations of LLMs have digested and encoded extensive knowledge about different human subpopulations and individuals, the hope is that these models can be trained, tuned or prompted to align with a wide range of different human perspectives. While researchers already evaluate the success of this alignment via surveys and tests, there is a lack of resources to evaluate the alignment on what oftentimes matters the most in NLP; the actual downstream tasks. To fill this gap we present SubData, a Python library that offers researchers working on topics related to subjectivity in annotation tasks a convenient way of collecting, combining and using a range of suitable datasets.

This paper presents rerankers, a Python library which provides an easy-to-use interface to the most commonly used re-ranking approaches. Re-ranking is an integral component of many retrieval pipelines; however, there exist numerous approaches to it, relying on different implementation methods. rerankers unifies these methods into a single user-friendly interface, allowing practitioners and researchers alike to explore different methods while only changing a single line of Python code. Moreover ,rerankers ensures that its implementations are done with the fewest dependencies possible, and re-uses the original implementation whenever possible, guaranteeing that our simplified interface results in no performance degradation compared to more complex ones. The full source code and list of supported models are updated regularly and available at https://github.com/answerdotai/rerankers.

Effective communication, specifically through documentation, is the beating heart of collaboration among contributors in software development. Recent advancements in language models (LMs) have enabled the introduction of a new type of actor in that ecosystem: LM-powered assistants capable of code generation, optimization, and maintenance. Our study investigates the efficacy of small language models (SLMs) for generating high-quality docstrings by assessing accuracy, conciseness, and clarity, benchmarking performance quantitatively through mathematical formulas and qualitatively through human evaluation using Likert scale. Further, we introduce DocuMint, as a large-scale supervised fine-tuning dataset with 100,000 samples. In quantitative experiments, Llama 3 8B achieved the best performance across all metrics, with conciseness and clarity scores of 0.605 and 64.88, respectively. However, under human evaluation, CodeGemma 7B achieved the highest overall score with an average of 8.3 out of 10 across all metrics. Fine-tuning the CodeGemma 2B model using the DocuMint dataset led to significant improvements in performance across all metrics, with gains of up to 22.5% in conciseness. The fine-tuned model and the dataset can be found in HuggingFace and the code can be found in the repository.

There have been growing discussions on estimating and subsequently reducing the operational carbon footprint of enterprise data centers. The design and intelligent control for data centers have an important impact on data center carbon footprint. In this paper, we showcase PyDCM, a Python library that enables extremely fast prototyping of data center design and applies reinforcement learning-enabled control with the purpose of evaluating key sustainability metrics including carbon footprint, energy consumption, and observing temperature hotspots. We demonstrate these capabilities of PyDCM and compare them to existing works in EnergyPlus for modeling data centers. PyDCM can also be used as a standalone Gymnasium environment for demonstrating sustainability-focused data center control.

Augmnety is a Python library for structured text augmentation. It is built on top of spaCy and allows for augmentation of both the text and its annotations. Augmenty provides a wide range of augmenters which can be combined in a flexible manner to create complex augmentation pipelines. It also includes a set of primitives that can be used to create custom augmenters such as word replacement augmenters. This functionality allows for augmentations within a range of applications such as named entity recognition (NER), part-of-speech tagging, and dependency parsing.

This paper introduces SCOPE-RL, a comprehensive open-source Python software designed for offline reinforcement learning (offline RL), off-policy evaluation (OPE), and selection (OPS). Unlike most existing libraries that focus solely on either policy learning or evaluation, SCOPE-RL seamlessly integrates these two key aspects, facilitating flexible and complete implementations of both offline RL and OPE processes. SCOPE-RL put particular emphasis on its OPE modules, offering a range of OPE estimators and robust evaluation-of-OPE protocols. This approach enables more in-depth and reliable OPE compared to other packages. For instance, SCOPE-RL enhances OPE by estimating the entire reward distribution under a policy rather than its mere point-wise expected value. Additionally, SCOPE-RL provides a more thorough evaluation-of-OPE by presenting the risk-return tradeoff in OPE results, extending beyond mere accuracy evaluations in existing OPE literature. SCOPE-RL is designed with user accessibility in mind. Its user-friendly APIs, comprehensive documentation, and a variety of easy-to-follow examples assist researchers and practitioners in efficiently implementing and experimenting with various offline RL methods and OPE estimators, tailored to their specific problem contexts. The documentation of SCOPE-RL is available at https://scope-rl.readthedocs.io/en/latest/.

Deep learning-based vision is characterized by intricate frameworks that often necessitate a profound understanding, presenting a barrier to newcomers and limiting broad adoption. With many researchers grappling with the constraints of smaller datasets, there's a pronounced reliance on pre-trained neural networks, especially for tasks such as image classification. This reliance is further intensified in niche imaging areas where obtaining vast datasets is challenging. Despite the widespread use of transfer learning as a remedy to the small dataset dilemma, a conspicuous absence of tailored auto-ML solutions persists. Addressing these challenges is "Deep Fast Vision", a python library that streamlines the deep learning process. This tool offers a user-friendly experience, enabling results through a simple nested dictionary definition, helping to democratize deep learning for non-experts. Designed for simplicity and scalability, Deep Fast Vision appears as a bridge, connecting the complexities of existing deep learning frameworks with the needs of a diverse user base.

Recent progress in natural language processing has been adapted to the symbolic music modality. Language models, such as Transformers, have been used with symbolic music for a variety of tasks among which music generation, modeling or transcription, with state-of-the-art performances. These models are beginning to be used in production products. To encode and decode music for the backbone model, they need to rely on tokenizers, whose role is to serialize music into sequences of distinct elements called tokens. MidiTok is an open-source library allowing to tokenize symbolic music with great flexibility and extended features. It features the most popular music tokenizations, under a unified API. It is made to be easily used and extensible for everyone.

TextDescriptives is a Python package for calculating a large variety of metrics from text. It is built on top of spaCy and can be easily integrated into existing workflows. The package has already been used for analysing the linguistic stability of clinical texts, creating features for predicting neuropsychiatric conditions, and analysing linguistic goals of primary school students. This paper describes the package and its features.

Introduction: Blood vessels can be non-invasively visualized from a digital fundus image (DFI). Several studies have shown an association between cardiovascular risk and vascular features obtained from DFI. Recent advances in computer vision and image segmentation enable automatising DFI blood vessel segmentation. There is a need for a resource that can automatically compute digital vasculature biomarkers (VBM) from these segmented DFI. Methods: In this paper, we introduce a Python Vasculature BioMarker toolbox, denoted PVBM. A total of 11 VBMs were implemented. In particular, we introduce new algorithmic methods to estimate tortuosity and branching angles. Using PVBM, and as a proof of usability, we analyze geometric vascular differences between glaucomatous patients and healthy controls. Results: We built a fully automated vasculature biomarker toolbox based on DFI segmentations and provided a proof of usability to characterize the vascular changes in glaucoma. For arterioles and venules, all biomarkers were significant and lower in glaucoma patients compared to healthy controls except for tortuosity, venular singularity length and venular branching angles. Conclusion: We have automated the computation of 11 VBMs from retinal blood vessel segmentation. The PVBM toolbox is made open source under a GNU GPL 3 license and is available on physiozoo.com (following publication).

Hyperdimensional computing (HD), also known as vector symbolic architectures (VSA), is a framework for computing with distributed representations by exploiting properties of random high-dimensional vector spaces. The commitment of the scientific community to aggregate and disseminate research in this particularly multidisciplinary area has been fundamental for its advancement. Joining these efforts, we present Torchhd, a high-performance open source Python library for HD/VSA. Torchhd seeks to make HD/VSA more accessible and serves as an efficient foundation for further research and application development. The easy-to-use library builds on top of PyTorch and features state-of-the-art HD/VSA functionality, clear documentation, and implementation examples from well-known publications. Comparing publicly available code with their corresponding Torchhd implementation shows that experiments can run up to 100x faster. Torchhd is available at: https://github.com/hyperdimensional-computing/torchhd.

Traditional machine learning systems are deployed under the closed-world setting, which requires the entire training data before the offline training process. However, real-world applications often face the incoming new classes, and a model should incorporate them continually. The learning paradigm is called Class-Incremental Learning (CIL). We propose a Python toolbox that implements several key algorithms for class-incremental learning to ease the burden of researchers in the machine learning community. The toolbox contains implementations of a number of founding works of CIL such as EWC and iCaRL, but also provides current state-of-the-art algorithms that can be used for conducting novel fundamental research. This toolbox, named PyCIL for Python Class-Incremental Learning, is available at https://github.com/G-U-N/PyCIL

Latte (for LATent Tensor Evaluation) is a Python library for evaluation of latent-based generative models in the fields of disentanglement learning and controllable generation. Latte is compatible with both PyTorch and TensorFlow/Keras, and provides both functional and modular APIs that can be easily extended to support other deep learning frameworks. Using NumPy-based and framework-agnostic implementation, Latte ensures reproducible, consistent, and deterministic metric calculations regardless of the deep learning framework of choice.

A large scale collection of both semantic and natural language resources is essential to leverage active Software Engineering research areas such as code reuse and code comprehensibility. Existing machine learning models ingest data from Open Source repositories (like GitHub projects) and forum discussions (like Stackoverflow.com), whereas, in this showcase, we took a step backward to orchestrate a corpus titled PyTorrent that contains 218,814 Python package libraries from PyPI and Anaconda environment. This is because earlier studies have shown that much of the code is redundant and Python packages from these environments are better in quality and are well-documented. PyTorrent enables users (such as data scientists, students, etc.) to build off the shelf machine learning models directly without spending months of effort on large infrastructure. The dataset, schema and a pretrained language model is available at: https://github.com/fla-sil/PyTorrent

Machine learning is a general-purpose technology holding promises for many interdisciplinary research problems. However, significant barriers exist in crossing disciplinary boundaries when most machine learning tools are developed in different areas separately. We present Pykale - a Python library for knowledge-aware machine learning on graphs, images, texts, and videos to enable and accelerate interdisciplinary research. We formulate new green machine learning guidelines based on standard software engineering practices and propose a novel pipeline-based application programming interface (API). PyKale focuses on leveraging knowledge from multiple sources for accurate and interpretable prediction, thus supporting multimodal learning and transfer learning (particularly domain adaptation) with latest deep learning and dimensionality reduction models. We build PyKale on PyTorch and leverage the rich PyTorch ecosystem. Our pipeline-based API design enforces standardization and minimalism, embracing green machine learning concepts via reducing repetitions and redundancy, reusing existing resources, and recycling learning models across areas. We demonstrate its interdisciplinary nature via examples in bioinformatics, knowledge graph, image/video recognition, and medical imaging.

Extracting opinions from texts has gathered a lot of interest in the last years, as we are experiencing an unprecedented volume of user-generated content in social networks and other places. A problem that social researchers find in using opinion mining tools is that they are usually behind commercial APIs and unavailable for other languages than English. To address these issues, we present pysentimiento, a multilingual Python toolkit for Sentiment Analysis and other Social NLP tasks. This open-source library brings state-of-the-art models for Spanish and English in a black-box fashion, allowing researchers to easily access these techniques.

In this paper, we present ManyTypes4Py, a large Python dataset for machine learning (ML)-based type inference. The dataset contains a total of 5,382 Python projects with more than 869K type annotations. Duplicate source code files were removed to eliminate the negative effect of the duplication bias. To facilitate training and evaluation of ML models, the dataset was split into training, validation and test sets by files. To extract type information from abstract syntax trees (ASTs), a lightweight static analyzer pipeline is developed and accompanied with the dataset. Using this pipeline, the collected Python projects were analyzed and the results of the AST analysis were stored in JSON-formatted files. The ManyTypes4Py dataset is shared on zenodo and its tools are publicly available on GitHub.

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 both simple classifiers and state-of-art chunk-based and online classifier ensembles. To improve computational efficiency, package utilises its own implementations of prediction metrics for imbalanced binary classification tasks.

A recently introduced text classifier, called SS3, has obtained state-of-the-art performance on the CLEF's eRisk tasks. SS3 was created to deal with risk detection over text streams and, therefore, not only supports incremental training and classification but also can visually explain its rationale. However, little attention has been paid to the potential use of SS3 as a general classifier. We believe this could be due to the unavailability of an open-source implementation of SS3. In this work, we introduce PySS3, a package that implements SS3 and also comes with visualization tools that allow researchers to deploy robust, explainable, and trusty machine learning models for text classification.

This paper presents the philosophy, design and feature-set of Neural Network Distiller, an open-source Python package for DNN compression research. Distiller is a library of DNN compression algorithms implementations, with tools, tutorials and sample applications for various learning tasks. Its target users are both engineers and researchers, and the rich content is complemented by a design-for-extensibility to facilitate new research. Distiller is open-source and is available on Github at https://github.com/NervanaSystems/distiller.

ProSper is a python library containing probabilistic algorithms to learn dictionaries. Given a set of data points, the implemented algorithms seek to learn the elementary components that have generated the data. The library widens the scope of dictionary learning approaches beyond implementations of standard approaches such as ICA, NMF or standard L1 sparse coding. The implemented algorithms are especially well-suited in cases when data consist of components that combine non-linearly and/or for data requiring flexible prior distributions. Furthermore, the implemented algorithms go beyond standard approaches by inferring prior and noise parameters of the data, and they provide rich a-posteriori approximations for inference. The library is designed to be extendable and it currently includes: Binary Sparse Coding (BSC), Ternary Sparse Coding (TSC), Discrete Sparse Coding (DSC), Maximal Causes Analysis (MCA), Maximum Magnitude Causes Analysis (MMCA), and Gaussian Sparse Coding (GSC, a recent spike-and-slab sparse coding approach). The algorithms are scalable due to a combination of variational approximations and parallelization. Implementations of all algorithms allow for parallel execution on multiple CPUs and multiple machines for medium to large-scale applications. Typical large-scale runs of the algorithms can use hundreds of CPUs to learn hundreds of dictionary elements from data with tens of millions of floating-point numbers such that models with several hundred thousand parameters can be optimized. The library is designed to have minimal dependencies and to be easy to use. It targets users of dictionary learning algorithms and Machine Learning researchers.

This paper presents a brief, semi-technical comparison of the essential features of the frequentist and Bayesian approaches to statistical inference, with several illustrative examples implemented in Python. The differences between frequentism and Bayesianism fundamentally stem from differing definitions of probability, a philosophical divide which leads to distinct approaches to the solution of statistical problems as well as contrasting ways of asking and answering questions about unknown parameters. After an example-driven discussion of these differences, we briefly compare several leading Python statistical packages which implement frequentist inference using classical methods and Bayesian inference using Markov Chain Monte Carlo.

The principles of automation and innovation serve as foundational elements for advancement in contemporary science and technology. Here, we introduce Pygen, an automation platform designed to empower researchers, technologists, and hobbyists to bring abstract ideas to life as core, usable software tools written in Python. Pygen leverages the immense power of autoregressive large language models to augment human creativity during the ideation, iteration, and innovation process. By combining state-of-the-art language models with open-source code generation technologies, Pygen has significantly reduced the manual overhead of tool development. From a user prompt, Pygen automatically generates Python packages for a complete workflow from concept to package generation and documentation. The findings of our work show that Pygen considerably enhances the researcher's productivity by enabling the creation of resilient, modular, and well-documented packages for various specialized purposes. We employ a prompt enhancement approach to distill the user's package description into increasingly specific and actionable. While being inherently an open-ended task, we have evaluated the generated packages and the documentation using Human Evaluation, LLM-based evaluation, and CodeBLEU, with detailed results in the results section. Furthermore, we documented our results, analyzed the limitations, and suggested strategies to alleviate them. Pygen is our vision of ethical automation, a framework that promotes inclusivity, accessibility, and collaborative development. This project marks the beginning of a large-scale effort towards creating tools where intelligent agents collaborate with humans to improve scientific and technological development substantially. Our code and generated examples are open-sourced at [https://github.com/GitsSaikat/Pygen]

scikit-image is an image processing library that implements algorithms and utilities for use in research, education and industry applications. It is released under the liberal "Modified BSD" open source license, provides a well-documented API in the Python programming language, and is developed by an active, international team of collaborators. In this paper we highlight the advantages of open source to achieve the goals of the scikit-image library, and we showcase several real-world image processing applications that use scikit-image.

With the advent of large language models (LLMs) like GPT-3, a natural question is the extent to which these models can be utilized for source code optimization. This paper presents methodologically stringent case studies applied to well-known open source python libraries pillow and numpy. We find that contemporary LLM ChatGPT-4 (state September and October 2023) is surprisingly adept at optimizing energy and compute efficiency. However, this is only the case in interactive use, with a human expert in the loop. Aware of experimenter bias, we document our qualitative approach in detail, and provide transcript and source code. We start by providing a detailed description of our approach in conversing with the LLM to optimize the _getextrema function in the pillow library, and a quantitative evaluation of the performance improvement. To demonstrate qualitative replicability, we report further attempts on another locus in the pillow library, and one code locus in the numpy library, to demonstrate generalization within and beyond a library. In all attempts, the performance improvement is significant (factor up to 38). We have also not omitted reporting of failed attempts (there were none). We conclude that LLMs are a promising tool for code optimization in open source libraries, but that the human expert in the loop is essential for success. Nonetheless, we were surprised by how few iterations were required to achieve substantial performance improvements that were not obvious to the expert in the loop. We would like bring attention to the qualitative nature of this study, more robust quantitative studies would need to introduce a layer of selecting experts in a representative sample -- we invite the community to collaborate.

We present PyThaiNLP, a free and open-source natural language processing (NLP) library for Thai language implemented in Python. It provides a wide range of software, models, and datasets for Thai language. We first provide a brief historical context of tools for Thai language prior to the development of PyThaiNLP. We then outline the functionalities it provided as well as datasets and pre-trained language models. We later summarize its development milestones and discuss our experience during its development. We conclude by demonstrating how industrial and research communities utilize PyThaiNLP in their work. The library is freely available at https://github.com/pythainlp/pythainlp.

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 programmers. We show the potential of the library by compiling nine public NER datasets into a unified format and evaluating the cross-domain and cross-lingual performance across the datasets. The results from our initial experiments show that in-domain performance is generally competitive across datasets. However, cross-domain generalization is challenging even with a large pretrained LM, which has nevertheless capacity to learn domain-specific features if fine-tuned on a combined dataset. To facilitate future research, we also release all our LM checkpoints via the Hugging Face model hub.

We present lambeq, the first high-level Python library for Quantum Natural Language Processing (QNLP). The open-source toolkit offers a detailed hierarchy of modules and classes implementing all stages of a pipeline for converting sentences to string diagrams, tensor networks, and quantum circuits ready to be used on a quantum computer. lambeq supports syntactic parsing, rewriting and simplification of string diagrams, ansatz creation and manipulation, as well as a number of compositional models for preparing quantum-friendly representations of sentences, employing various degrees of syntax sensitivity. We present the generic architecture and describe the most important modules in detail, demonstrating the usage with illustrative examples. Further, we test the toolkit in practice by using it to perform a number of experiments on simple NLP tasks, implementing both classical and quantum pipelines.

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 library supports training deep learning models created either with PyGAD itself or with frameworks like Keras and PyTorch. Given its stable state, PyGAD is also in active development to respond to the user's requested features and enhancement received on GitHub https://github.com/ahmedfgad/GeneticAlgorithmPython. PyGAD comes with documentation https://pygad.readthedocs.io for further details and examples.

River is a machine learning library for dynamic data streams and continual learning. It provides multiple state-of-the-art learning methods, data generators/transformers, performance metrics and evaluators for different stream learning problems. It is the result from the merger of the two most popular packages for stream learning in Python: Creme and scikit-multiflow. River introduces a revamped architecture based on the lessons learnt from the seminal packages. River's ambition is to be the go-to library for doing machine learning on streaming data. Additionally, this open source package brings under the same umbrella a large community of practitioners and researchers. The source code is available at https://github.com/online-ml/river.

PySAD is an open-source python framework for anomaly detection on streaming data. PySAD serves various state-of-the-art methods for streaming anomaly detection. The framework provides a complete set of tools to design anomaly detection experiments ranging from projectors to probability calibrators. PySAD builds upon popular open-source frameworks such as PyOD and scikit-learn. We enforce software quality by enforcing compliance with PEP8 guidelines, functional testing and using continuous integration. The source code is publicly available on https://github.com/selimfirat/pysad.

metric-learn is an open source Python package implementing supervised and weakly-supervised distance metric learning algorithms. As part of scikit-learn-contrib, it provides a unified interface compatible with scikit-learn which allows to easily perform cross-validation, model selection, and pipelining with other machine learning estimators. metric-learn is thoroughly tested and available on PyPi under the MIT licence.

With the recent focus on Large Language Models (LLMs), both StarCoder (Li et al., 2023) and Code Llama (Rozi\`ere et al., 2023) have demonstrated remarkable performance in code generation. However, there is still a need for improvement in code translation functionality with efficient training techniques. In response to this, we introduce SteloCoder, a decoder-only StarCoder-based LLM designed specifically for multi-programming language-to-Python code translation. In particular, SteloCoder achieves C++, C#, JavaScript, Java, or PHP-to-Python code translation without specifying the input programming language. We modified StarCoder model architecture by incorporating a Mixture-of-Experts (MoE) technique featuring five experts and a gating network for multi-task handling. Experts are obtained by StarCoder fine-tuning. Specifically, we use a Low-Rank Adaptive Method (LoRA) technique, limiting each expert size as only 0.06% of number of StarCoder's parameters. At the same time, to enhance training efficiency in terms of time, we adopt curriculum learning strategy and use self-instruct data for efficient fine-tuning. As a result, each expert takes only 6 hours to train on one single 80Gb A100 HBM. With experiments on XLCoST datasets, SteloCoder achieves an average of 73.76 CodeBLEU score in multi-programming language-to-Python translation, surpassing the top performance from the leaderboard by at least 3.5. This accomplishment is attributed to only 45M extra parameters with StarCoder as the backbone and 32 hours of valid training on one 80GB A100 HBM. The source code is release here: https://github.com/sade-adrien/SteloCoder.

We introduce small-text, an easy-to-use active learning library, which offers pool-based active learning for single- and multi-label text classification in Python. It features numerous pre-implemented state-of-the-art query strategies, including some that leverage the GPU. Standardized interfaces allow the combination of a variety of classifiers, query strategies, and stopping criteria, facilitating a quick mix and match, and enabling a rapid and convenient development of both active learning experiments and applications. With the objective of making various classifiers and query strategies accessible for active learning, small-text integrates several well-known machine learning libraries, namely scikit-learn, PyTorch, and Hugging Face transformers. The latter integrations are optionally installable extensions, so GPUs can be used but are not required. Using this new library, we investigate the performance of the recently published SetFit training paradigm, which we compare to vanilla transformer fine-tuning, finding that it matches the latter in classification accuracy while outperforming it in area under the curve. The library is available under the MIT License at https://github.com/webis-de/small-text, in version 1.3.0 at the time of writing.

Many works have recently proposed the use of Large Language Model (LLM) based agents for performing `repository level' tasks, loosely defined as a set of tasks whose scopes are greater than a single file. This has led to speculation that the orchestration of these repository-level tasks could lead to software engineering agents capable of performing almost independently of human intervention. However, of the suite of tasks that would need to be performed by this autonomous software engineering agent, we argue that one important task is missing, which is to fulfil project level dependency by installing other repositories. To investigate the feasibility of this repository level installation task, we introduce a benchmark of of repository installation tasks curated from 40 open source Python projects, which includes a ground truth installation process for each target repository. Further, we propose Installamatic, an agent which aims to perform and verify the installation of a given repository by searching for relevant instructions from documentation in the repository. Empirical experiments reveal that that 55% of the studied repositories can be automatically installed by our agent at least one out of ten times. Through further analysis, we identify the common causes for our agent's inability to install a repository, discuss the challenges faced in the design and implementation of such an agent and consider the implications that such an agent could have for developers.

As one of the most popular dynamic languages, Python experiences a decrease in readability and maintainability when code smells are present. Recent advancements in Large Language Models have sparked growing interest in AI-enabled tools for both code generation and refactoring. GitHub Copilot is one such tool that has gained widespread usage. Copilot Chat, released on September 2023, functions as an interactive tool aims at facilitating natural language-powered coding. However, limited attention has been given to understanding code smells in Copilot-generated Python code and Copilot's ability to fix the code smells it generates. To this end, we built a dataset comprising 102 code smells in Copilot-generated Python code. Our aim is to first explore the occurrence of code smells in Copilot-generated Python code and then evaluate the effectiveness of Copilot in fixing these code smells employing different prompts. The results show that 8 out of 10 types of Python smells can be detected in Copilot-generated Python code, among which Multiply-Nested Container is the most common one. For these code smells, Copilot Chat achieves a highest fixing rate of 87.1%, showing promise in fixing Python code smells generated by Copilot itself. Besides, the effectiveness of Copilot Chat in fixing these smells can be improved with the provision of more detailed prompts. However, using Copilot Chat to fix these smells might introduce new code smells.

As with any physical instrument, hyperspectral cameras induce different kinds of noise in the acquired data. Therefore, Hyperspectral denoising is a crucial step for analyzing hyperspectral images (HSIs). Conventional computational methods rarely use GPUs to improve efficiency and are not fully open-source. Alternatively, deep learning-based methods are often open-source and use GPUs, but their training and utilization for real-world applications remain non-trivial for many researchers. Consequently, we propose HyDe: the first open-source, GPU-accelerated Python-based, hyperspectral image denoising toolbox, which aims to provide a large set of methods with an easy-to-use environment. HyDe includes a variety of methods ranging from low-rank wavelet-based methods to deep neural network (DNN) models. HyDe's interface dramatically improves the interoperability of these methods and the performance of the underlying functions. In fact, these methods maintain similar HSI denoising performance to their original implementations while consuming nearly ten times less energy. Furthermore, we present a method for training DNNs for denoising HSIs which are not spatially related to the training dataset, i.e., training on ground-level HSIs for denoising HSIs with other perspectives including airborne, drone-borne, and space-borne. To utilize the trained DNNs, we show a sliding window method to effectively denoise HSIs which would otherwise require more than 40 GB. The package can be found at: https://github.com/Helmholtz-AI-Energy/HyDe.

Large language models have the potential to be valuable in the healthcare industry, but it's crucial to verify their safety and effectiveness through rigorous evaluation. For this purpose, we comprehensively evaluated both open-source LLMs and Google's new multimodal LLM called Gemini across Medical reasoning, hallucination detection, and Medical Visual Question Answering tasks. While Gemini showed competence, it lagged behind state-of-the-art models like MedPaLM 2 and GPT-4 in diagnostic accuracy. Additionally, Gemini achieved an accuracy of 61.45\% on the medical VQA dataset, significantly lower than GPT-4V's score of 88\%. Our analysis revealed that Gemini is highly susceptible to hallucinations, overconfidence, and knowledge gaps, which indicate risks if deployed uncritically. We also performed a detailed analysis by medical subject and test type, providing actionable feedback for developers and clinicians. To mitigate risks, we applied prompting strategies that improved performance. Additionally, we facilitated future research and development by releasing a Python module for medical LLM evaluation and establishing a dedicated leaderboard on Hugging Face for medical domain LLMs. Python module can be found at https://github.com/promptslab/RosettaEval

Empirical risk minimization (ERM) with a computationally feasible surrogate loss is a widely accepted approach for classification. Notably, the convexity and calibration (CC) properties of a loss function ensure consistency of ERM in maximizing accuracy, thereby offering a wide range of options for surrogate losses. In this article, we propose a novel ensemble method, namely EnsLoss, which extends the ensemble learning concept to combine loss functions within the ERM framework. A key feature of our method is the consideration on preserving the "legitimacy" of the combined losses, i.e., ensuring the CC properties. Specifically, we first transform the CC conditions of losses into loss-derivatives, thereby bypassing the need for explicit loss functions and directly generating calibrated loss-derivatives. Therefore, inspired by Dropout, EnsLoss enables loss ensembles through one training process with doubly stochastic gradient descent (i.e., random batch samples and random calibrated loss-derivatives). We theoretically establish the statistical consistency of our approach and provide insights into its benefits. The numerical effectiveness of EnsLoss compared to fixed loss methods is demonstrated through experiments on a broad range of 14 OpenML tabular datasets and 46 image datasets with various deep learning architectures. Python repository and source code are available on GitHub at https://github.com/statmlben/ensloss.

This thesis explores open-sourced machine learning (ML) model explanation tools to understand whether these tools can allow a layman to visualize, understand, and suggest intuitive remedies to unfairness in ML-based decision-support systems. Machine learning models trained on datasets biased against minority groups are increasingly used to guide life-altering social decisions, prompting the urgent need to study their logic for unfairness. Due to this problem's impact on vast populations of the general public, it is critical for the layperson -- not just subject matter experts in social justice or machine learning experts -- to understand the nature of unfairness within these algorithms and the potential trade-offs. Existing research on fairness in machine learning focuses mostly on the mathematical definitions and tools to understand and remedy unfair models, with some directly citing user-interactive tools as necessary for future work. This thesis presents FairLay-ML, a proof-of-concept GUI integrating some of the most promising tools to provide intuitive explanations for unfair logic in ML models by integrating existing research tools (e.g. Local Interpretable Model-Agnostic Explanations) with existing ML-focused GUI (e.g. Python Streamlit). We test FairLay-ML using models of various accuracy and fairness generated by an unfairness detector tool, Parfait-ML, and validate our results using Themis. Our study finds that the technology stack used for FairLay-ML makes it easy to install and provides real-time black-box explanations of pre-trained models to users. Furthermore, the explanations provided translate to actionable remedies.

Though LLMs are capable of generating plausible programs, it's challenging to interact with the LLMs further to revise the program, especially if the user's specific requirements are different from the initial proposal. In this paper, we introduce ANPL, an interactive programming system that ensures users can always refine the generated code towards their specific programmatic intents via structured decompositions. Borrowing the paradigm of sketching from program synthesis, an ANPL program consists of a set of input-outputs that it must satisfy, a ``sketch'' -- control/data flow expressed in precise code (e.g. Python), and ``holes'' -- sub-modules to be implemented by the LLM specified with natural language. The user revises an ANPL program by either modifying the sketch, changing the language used to describe the holes, or providing additional input-outputs to a particular hole, turning it into a sub-ANPL program that can be solved recursively. This workflow allows the users to offload programming burdens to the LLM as much as possible while retaining the ability to pinpoint and resolve bugs locally, without exposing the rest of the program to the LLM. We deploy ANPL on the Abstraction and Reasoning Corpus (ARC), a set of unique tasks that are challenging for state-of-the-art AI systems, showing it outperforms baseline programming systems that (a) without the ability to decompose tasks interactively and (b) without the guarantee that the modules can be correctly composed together. Additional evaluations on APPS, HumanEval, and real-world programming tasks have validated that the ANPL framework is applicable to multiple programming domains. We release the ANPL solutions to the ARC tasks as a dataset, providing insights into how humans decompose novel tasks programmatically. See our code at https://iprc-dip.github.io/ANPL/.

How can we perform computations over natural language representations to solve tasks that require symbolic and numeric reasoning? We propose natural language embedded programs (NLEP) as a unifying framework for addressing math/symbolic reasoning, natural language understanding, and instruction following tasks. Our approach prompts a language model to generate full Python programs that define functions over data structures which contain natural language representations of structured knowledge. A Python interpreter then executes the generated code and prints the output. Despite using a task-general prompt, we find that this approach can improve upon strong baselines across a range of different tasks including math and symbolic reasoning, text classification, question answering, and instruction following. We further find the generated programs are often interpretable and enable post-hoc verification of the intermediate reasoning steps.

This paper presents an experience report on the development of Retrieval Augmented Generation (RAG) systems using PDF documents as the primary data source. The RAG architecture combines generative capabilities of Large Language Models (LLMs) with the precision of information retrieval. This approach has the potential to redefine how we interact with and augment both structured and unstructured knowledge in generative models to enhance transparency, accuracy, and contextuality of responses. The paper details the end-to-end pipeline, from data collection, preprocessing, to retrieval indexing and response generation, highlighting technical challenges and practical solutions. We aim to offer insights to researchers and practitioners developing similar systems using two distinct approaches: OpenAI's Assistant API with GPT Series and Llama's open-source models. The practical implications of this research lie in enhancing the reliability of generative AI systems in various sectors where domain-specific knowledge and real-time information retrieval is important. The Python code used in this work is also available at: https://github.com/GPT-Laboratory/RAG-LLM-Development-Guidebook-from-PDFs.

Conversational data is essential in psychology because it can help researchers understand individuals cognitive processes, emotions, and behaviors. Utterance labelling is a common strategy for analyzing this type of data. The development of NLP algorithms allows researchers to automate this task. However, psychological conversational data present some challenges to NLP researchers, including multilabel classification, a large number of classes, and limited available data. This study explored how automated labels generated by NLP methods are comparable to human labels in the context of conversations on adulthood transition. We proposed strategies to handle three common challenges raised in psychological studies. Our findings showed that the deep learning method with domain adaptation (RoBERTa-CON) outperformed all other machine learning methods; and the hierarchical labelling system that we proposed was shown to help researchers strategically analyze conversational data. Our Python code and NLP model are available at https://github.com/mlaricheva/automated_labeling.

Machine learning-based program analyses have recently shown the promise of integrating formal and probabilistic reasoning towards aiding software development. However, in the absence of large annotated corpora, training these analyses is challenging. Towards addressing this, we present BugLab, an approach for self-supervised learning of bug detection and repair. BugLab co-trains two models: (1) a detector model that learns to detect and repair bugs in code, (2) a selector model that learns to create buggy code for the detector to use as training data. A Python implementation of BugLab improves by up to 30% upon baseline methods on a test dataset of 2374 real-life bugs and finds 19 previously unknown bugs in open-source software.

A transcompiler, also known as source-to-source translator, is a system that converts source code from a high-level programming language (such as C++ or Python) to another. Transcompilers are primarily used for interoperability, and to port codebases written in an obsolete or deprecated language (e.g. COBOL, Python 2) to a modern one. They typically rely on handcrafted rewrite rules, applied to the source code abstract syntax tree. Unfortunately, the resulting translations often lack readability, fail to respect the target language conventions, and require manual modifications in order to work properly. The overall translation process is timeconsuming and requires expertise in both the source and target languages, making code-translation projects expensive. Although neural models significantly outperform their rule-based counterparts in the context of natural language translation, their applications to transcompilation have been limited due to the scarcity of parallel data in this domain. In this paper, we propose to leverage recent approaches in unsupervised machine translation to train a fully unsupervised neural transcompiler. We train our model on source code from open source GitHub projects, and show that it can translate functions between C++, Java, and Python with high accuracy. Our method relies exclusively on monolingual source code, requires no expertise in the source or target languages, and can easily be generalized to other programming languages. We also build and release a test set composed of 852 parallel functions, along with unit tests to check the correctness of translations. We show that our model outperforms rule-based commercial baselines by a significant margin.

Strategies for the generation of periodic discrete structures with identical two-point correlation are developed. Starting from a pair of root structures, which are not related by translation, phase inversion or axis reflections, child structures of arbitrary resolution (i.e., pixel or voxel numbers) and number of phases (i.e., material phases/species) can be generated by means of trivial embedding based phase extension, application of kernels and/or phase coalescence, such that the generated structures inherit the two-point-correlation equivalence. Proofs of the inheritance property are provided by means of the Discrete Fourier Transform theory. A Python 3 implementation of the results is offered by the authors through the Github repository https://github.com/DataAnalyticsEngineering/EQ2PC in order to make the provided results reproducible and useful for all interested readers. Examples for the generation of structures are demonstrated, together with applications in the homogenization theory of periodic media.