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Jupyter notebooks have become central in data science, integrating code, text and output in a flexible environment. With the rise of machine learning (ML), notebooks are increasingly used for ML prototyping and data analysis. However, due to their dependence on complex ML libraries and the flexible notebook semantics that allow cells to be run in any order, notebooks are susceptible to software bugs that may lead to program crashes. This paper presents a comprehensive empirical study focused on crashes in ML notebooks. We collect 64,031 ML notebooks containing 92,542 crashes from GitHub and Kaggle, and manually analyze a sample of 746 crashes across various aspects, including exception types and root causes. Our analysis highlights unique root causes related to notebook semantics, including out-of-order execution and previous cell error, that have not been thoroughly covered in earlier research. Furthermore, we categorize crashes as ML bugs or general Python bugs and examine how the crashes are distributed across different stages of the ML pipeline. Our analysis reveals that 87% of crashes are caused by API misuse, data confusion, notebook-specific issues, environment problems, and implementation errors. Crashes are more commonly related to ML bugs than general Python bugs, particularly in Kaggle notebooks, where over 70% of crashes are ML-related. The distribution of crashes across ML pipeline stages differs between the two platforms. Additionally, most crashes (58%) occur during data preparation, model training, and evaluation/prediction stages of the ML pipeline. GitHub and Kaggle exhibit different crash distributions across these stages., Comment: submitted to a journal

Motivation: Automated bug detection in dynamically typed languages such as Python is essential for maintaining code quality. The lack of mandatory type annotations in such languages can lead to errors that are challenging to identify early with traditional static analysis tools. Recent progress in deep neural networks has led to increased use of neural bug detectors. In statically typed languages, a type checker is integrated into the compiler and thus taken into consideration when the neural bug detector is designed for these languages. Problem: However, prior studies overlook this aspect during the training and testing of neural bug detectors for dynamically typed languages. When an optional type checker is used, assessing existing neural bug detectors on bugs easily detectable by type checkers may impact their performance estimation. Moreover, including these bugs in the training set of neural bug detectors can shift their detection focus toward the wrong type of bugs. Contribution: We explore the impact of type checking on various neural bug detectors for variable misuse bugs, a common type targeted by neural bug detectors. Existing synthetic and real-world datasets are type-checked to evaluate the prevalence of type-related bugs. Then, we investigate how type-related bugs influence the training and testing of the neural bug detectors. Findings: Our findings indicate that existing bug detection datasets contain a significant proportion of type-related bugs. Building on this insight, we discover integrating the neural bug detector with a type checker can be beneficial, especially when the code is annotated with types. Further investigation reveals neural bug detectors perform better on type-related bugs than other bugs. Moreover, removing type-related bugs from the training data helps improve neural bug detectors' ability to identify bugs beyond the scope of type checkers., Comment: Accepted by ICSE'25 Research Track

Language models of code have demonstrated state-of-the-art performance across various software engineering and source code analysis tasks. However, their demanding computational resource requirements and consequential environmental footprint remain as significant challenges. This work introduces ALPINE, an adaptive programming language-agnostic pruning technique designed to substantially reduce these models' computational overhead. The proposed method offers a pluggable layer that can be integrated with all Transformer-based models. With ALPINE, input sequences undergo adaptive compression throughout the pipeline, reaching a size up to $\times 3$ less their initial size, resulting in significantly reduced computational load. Our experiments on two software engineering tasks, defect prediction and code clone detection across three language models CodeBERT, GraphCodeBERT and UniXCoder show that ALPINE achieves up to a 50% reduction in FLOPs, a 58.1% decrease in memory footprint, and a 28.1% improvement in throughput on average. This led to a reduction in CO2 by up to $44.85$%. Importantly, it achieves the reduction in computation resources while maintaining up to 98.1% of the original predictive performance. These findings highlight the potential of ALPINE in making language models of code more resource-efficient and accessible while preserving their performance, contributing to the overall sustainability of adopting language models in software development. Also, it sheds light on redundant and noisy information in source code analysis corpora, as shown by the substantial sequence compression achieved by ALPINE., Comment: Accepted to the The ACM International Conference on the Foundations of Software Engineering (FSE) (FSE 2025)

Motivation. Large language models (LLMs) have exhibited remarkable proficiency in diverse software engineering (SE) tasks. Handling such tasks typically involves acquiring foundational coding knowledge on large, general-purpose datasets during a pre-training phase, and subsequently refining on smaller, task-specific datasets as part of a fine-tuning phase. Problem statement. While intra-dataset code duplication examines the intersection between the training and test splits within a given dataset and has been addressed in prior research, inter-dataset code duplication, which gauges the overlap between different datasets, remains largely unexplored. If this phenomenon exists, it could compromise the integrity of LLM evaluations because of the inclusion of fine-tuning test samples that were already encountered during pre-training, resulting in inflated performance metrics. Contribution. This paper explores the phenomenon of inter-dataset code duplication and its impact on evaluating LLMs across diverse SE tasks. Study design. We conduct an empirical study using the CodeSearchNet dataset (CSN), a widely adopted pre-training dataset, and five fine-tuning datasets used for various se tasks. We first identify the intersection between the pre-training and fine-tuning datasets using a deduplication process. Next, we pre-train two versions of LLMs using a subset of CSN: one leaky LLM and one non-leaky LLM. Finally, we fine-tune both models and compare their performances using leaky fine-tuning test samples. Results. Our findings reveal a potential threat to the evaluation of LLMs across multiple SE tasks, stemming from the inter-dataset code duplication phenomenon. We also demonstrate that this threat is accentuated by the chosen fine-tuning technique. Furthermore, we provide evidence that open-source models could be affected by inter-dataset duplication.

The objective of pre-trained language models is to learn contextual representations of textual data. Pre-trained language models have become mainstream in natural language processing and code modeling. Using probes, a technique to study the linguistic properties of hidden vector spaces, previous works have shown that these pre-trained language models encode simple linguistic properties in their hidden representations. However, none of the previous work assessed whether these models encode the whole grammatical structure of a programming language. In this paper, we prove the existence of a syntactic subspace, lying in the hidden representations of pre-trained language models, which contain the syntactic information of the programming language. We show that this subspace can be extracted from the models' representations and define a novel probing method, the AST-Probe, that enables recovering the whole abstract syntax tree (AST) of an input code snippet. In our experimentations, we show that this syntactic subspace exists in five state-of-the-art pre-trained language models. In addition, we highlight that the middle layers of the models are the ones that encode most of the AST information. Finally, we estimate the optimal size of this syntactic subspace and show that its dimension is substantially lower than those of the models' representation spaces. This suggests that pre-trained language models use a small part of their representation spaces to encode syntactic information of the programming languages.

The availability of shared software models provides opportunities for reusing, adapting and learning from them. Public models are typically stored in a variety of locations, including model repositories, regular source code repositories, web pages, etc. To profit from them developers need effective search mechanisms to locate the models relevant for their tasks. However, to date, there has been little success in creating a generic and efficient search engine specially tailored to the modelling domain. In this paper we present MAR, a search engine for models. MAR is generic in the sense that it can index any type of model if its meta-model is known. MAR uses a query-by-example approach, that is, it uses example models as queries. The search takes the model structure into account using the notion of bag of paths, which encodes the structure of a model using paths between model elements and is a representation amenable for indexing. MAR is built over HBase using a specific design to deal with large repositories. Our benchmarks show that the engine is efficient and has fast response times in most cases. We have also evaluated the precision of the search engine by creating model mutants which simulate user queries. A REST API is available to perform queries and an Eclipse plug-in allows end users to connect to the search engine from model editors. We have currently indexed more than 50.000 models of different kinds, including Ecore meta-models, BPMN diagrams and UML models. MAR is available at http://mar-search.org.