Daily Papers

We introduce Biomaker CA: a Biome Maker project using Cellular Automata (CA). In Biomaker CA, morphogenesis is a first class citizen and small seeds need to grow into plant-like organisms to survive in a nutrient starved environment and eventually reproduce with variation so that a biome survives for long timelines. We simulate complex biomes by means of CA rules in 2D grids and parallelize all of its computation on GPUs through the Python JAX framework. We show how this project allows for several different kinds of environments and laws of 'physics', alongside different model architectures and mutation strategies. We further analyze some configurations to show how plant agents can grow, survive, reproduce, and evolve, forming stable and unstable biomes. We then demonstrate how one can meta-evolve models to survive in a harsh environment either through end-to-end meta-evolution or by a more surgical and efficient approach, called Petri dish meta-evolution. Finally, we show how to perform interactive evolution, where the user decides how to evolve a plant model interactively and then deploys it in a larger environment. We open source Biomaker CA at: https://tinyurl.com/2x8yu34s .

We describe the design and commissioning tests for the DSA-110 Not-So-Fast Radio Burst (NSFRB) search pipeline, a 1.4 GHz image-plane single-pulse search sensitive to 134 ms-160.8 s radio bursts. Extending the pulse width range of the Fast Radio Burst (FRB) search by 3 orders of magnitude, the NSFRB search is sensitive to the recently-discovered Galactic Long Period Radio Transients (LPRTs). The NSFRB search operates in real-time, utilizing a custom GPU-accelerated search code, cerberus, implemented in Python with JAX. We summarize successful commissioning sensitivity tests with continuum sources and pulsar B0329+54, estimating the 6sigma flux (fluence) threshold to be ~290 mJy (~40 Jy ms). Future tests of recovery of longer timescale transients, e.g. CHIME J1634+44, are planned to supplement injection testing and B0329+54 observations. An offline DSA-110 NSFRB Galactic Plane Survey was conducted to search for LPRTs, covering -3.5^circ<b<5.7^circ and 141^circ<l<225^circ (~770 square degrees) in Galactic coordinates. We estimate an upper limit Poissonian burst rate ~1 hr^{-1} per square degree (~7 hr^{-1} per 3^circtimes3^circ survey grid cell) maximized across the inner |b|<0.25^circ of the surveyed region. By imposing the ~290 mJy flux limit on two representative models (the magnetar plastic flow model and the White Dwarf-M Dwarf binary model), we reject with 95% confidence the presence of White Dwarf-M Dwarf binary LPRTs with periods between ~10-70s within ~95% of the surveyed region. Combined with the prevalence of LPRTs in the Galactic Plane, our results motivate further consideration of both White Dwarf-M Dwarf binary models and isolated magnetar models. We will continue to explore novel LPRT search strategies during real-time operations, such as triggered periodicity searches and additional targeted surveys.

We extend JAX with the capability to automatically differentiate higher-order functions (functionals and operators). By representing functions as a generalization of arrays, we seamlessly use JAX's existing primitive system to implement higher-order functions. We present a set of primitive operators that serve as foundational building blocks for constructing several key types of functionals. For every introduced primitive operator, we derive and implement both linearization and transposition rules, aligning with JAX's internal protocols for forward and reverse mode automatic differentiation. This enhancement allows for functional differentiation in the same syntax traditionally use for functions. The resulting functional gradients are themselves functions ready to be invoked in python. We showcase this tool's efficacy and simplicity through applications where functional derivatives are indispensable. The source code of this work is released at https://github.com/sail-sg/autofd .

Continual Learning is an important and challenging problem in machine learning, where models must adapt to a continuous stream of new data without forgetting previously acquired knowledge. While existing frameworks are built on PyTorch, the rising popularity of JAX might lead to divergent codebases, ultimately hindering reproducibility and progress. To address this problem, we introduce SequeL, a flexible and extensible library for Continual Learning that supports both PyTorch and JAX frameworks. SequeL provides a unified interface for a wide range of Continual Learning algorithms, including regularization-based approaches, replay-based approaches, and hybrid approaches. The library is designed towards modularity and simplicity, making the API suitable for both researchers and practitioners. We release SequeL\url{https://github.com/nik-dim/sequel} as an open-source library, enabling researchers and developers to easily experiment and extend the library for their own purposes.

Program synthesis strives to generate a computer program as a solution to a given problem specification, expressed with input-output examples or natural language descriptions. The prevalence of large language models advances the state-of-the-art for program synthesis, though limited training resources and data impede open access to such models. To democratize this, we train and release a family of large language models up to 16.1B parameters, called CODEGEN, on natural language and programming language data, and open source the training library JAXFORMER. We show the utility of the trained model by demonstrating that it is competitive with the previous state-of-the-art on zero-shot Python code generation on HumanEval. We further investigate the multi-step paradigm for program synthesis, where a single program is factorized into multiple prompts specifying subproblems. To this end, we construct an open benchmark, Multi-Turn Programming Benchmark (MTPB), consisting of 115 diverse problem sets that are factorized into multi-turn prompts. Our analysis on MTPB shows that the same intent provided to CODEGEN in multi-turn fashion significantly improves program synthesis over that provided as a single turn. We make the training library JAXFORMER and model checkpoints available as open source contribution: https://github.com/salesforce/CodeGen.

Bayesian models of cognition have gained considerable traction in computational neuroscience and psychiatry. Their scopes are now expected to expand rapidly to artificial intelligence, providing general inference frameworks to support embodied, adaptable, and energy-efficient autonomous agents. A central theory in this domain is predictive coding, which posits that learning and behaviour are driven by hierarchical probabilistic inferences about the causes of sensory inputs. Biological realism constrains these networks to rely on simple local computations in the form of precision-weighted predictions and prediction errors. This can make this framework highly efficient, but its implementation comes with unique challenges on the software development side. Embedding such models in standard neural network libraries often becomes limiting, as these libraries' compilation and differentiation backends can force a conceptual separation between optimization algorithms and the systems being optimized. This critically departs from other biological principles such as self-monitoring, self-organisation, cellular growth and functional plasticity. In this paper, we introduce pyhgf: a Python package backed by JAX and Rust for creating, manipulating and sampling dynamic networks for predictive coding. We improve over other frameworks by enclosing the network components as transparent, modular and malleable variables in the message-passing steps. The resulting graphs can implement arbitrary computational complexities as beliefs propagation. But the transparency of core variables can also translate into inference processes that leverage self-organisation principles, and express structure learning, meta-learning or causal discovery as the consequence of network structural adaptation to surprising inputs. The code, tutorials and documentation are hosted at: https://github.com/ilabcode/pyhgf.

Benchmarks play a crucial role in the development and analysis of reinforcement learning (RL) algorithms. We identify that existing benchmarks used for research into open-ended learning fall into one of two categories. Either they are too slow for meaningful research to be performed without enormous computational resources, like Crafter, NetHack and Minecraft, or they are not complex enough to pose a significant challenge, like Minigrid and Procgen. To remedy this, we first present Craftax-Classic: a ground-up rewrite of Crafter in JAX that runs up to 250x faster than the Python-native original. A run of PPO using 1 billion environment interactions finishes in under an hour using only a single GPU and averages 90% of the optimal reward. To provide a more compelling challenge we present the main Craftax benchmark, a significant extension of the Crafter mechanics with elements inspired from NetHack. Solving Craftax requires deep exploration, long term planning and memory, as well as continual adaptation to novel situations as more of the world is discovered. We show that existing methods including global and episodic exploration, as well as unsupervised environment design fail to make material progress on the benchmark. We believe that Craftax can for the first time allow researchers to experiment in a complex, open-ended environment with limited computational resources.

We present a feasibility-seeking approach to neural network training. This mathematical optimization framework is distinct from conventional gradient-based loss minimization and uses projection operators and iterative projection algorithms. We reformulate training as a large-scale feasibility problem: finding network parameters and states that satisfy local constraints derived from its elementary operations. Training then involves projecting onto these constraints, a local operation that can be parallelized across the network. We introduce PJAX, a JAX-based software framework that enables this paradigm. PJAX composes projection operators for elementary operations, automatically deriving the solution operators for the feasibility problems (akin to autodiff for derivatives). It inherently supports GPU/TPU acceleration, provides a familiar NumPy-like API, and is extensible. We train diverse architectures (MLPs, CNNs, RNNs) on standard benchmarks using PJAX, demonstrating its functionality and generality. Our results show that this approach is as a compelling alternative to gradient-based training, with clear advantages in parallelism and the ability to handle non-differentiable operations.

Low-precision formats such as float8 have been introduced in machine learning accelerated hardware to improve computational efficiency for large language models training and inference. Nevertheless, adoption by the ML community has been slowed down by the complex, and sometimes brittle, techniques required to match higher precision training accuracy. In this work, we present Scalify, a end-to-end scale propagation paradigm for computational graphs, generalizing and formalizing existing tensor scaling methods. Experiment results show that Scalify supports out-of-the-box float8 matrix multiplication and gradients representation, as well as float16 optimizer state storage. Our JAX implementation of Scalify is open-sourced at https://github.com/graphcore-research/jax-scalify

We propose MUltiway Dynamic Dense (MUDD) connections, a simple yet effective method to address the limitations of residual connections and enhance cross-layer information flow in Transformers. Unlike existing dense connection approaches with static and shared connection weights, MUDD generates connection weights dynamically depending on hidden states at each sequence position and for each decoupled input stream (the query, key, value or residual) of a Transformer block. MUDD connections can be seamlessly integrated into any Transformer architecture to create MUDDFormer. Extensive experiments show that MUDDFormer significantly outperforms Transformers across various model architectures and scales in language modeling, achieving the performance of Transformers trained with 1.8X-2.4X compute. Notably, MUDDPythia-2.8B matches Pythia-6.9B in pretraining ppl and downstream tasks and even rivals Pythia-12B in five-shot settings, while adding only 0.23% parameters and 0.4% computation. Code in JAX and PyTorch and pre-trained models are available at https://github.com/Caiyun-AI/MUDDFormer .

We present FAX, a JAX-based library designed to support large-scale distributed and federated computations in both data center and cross-device applications. FAX leverages JAX's sharding mechanisms to enable native targeting of TPUs and state-of-the-art JAX runtimes, including Pathways. FAX embeds building blocks for federated computations as primitives in JAX. This enables three key benefits. First, FAX computations can be translated to XLA HLO. Second, FAX provides a full implementation of federated automatic differentiation, greatly simplifying the expression of federated computations. Last, FAX computations can be interpreted out to existing production cross-device federated compute systems. We show that FAX provides an easily programmable, performant, and scalable framework for federated computations in the data center. FAX is available at https://github.com/google-research/google-research/tree/master/fax .

In this paper we present a Java-to-Python (J2P) and Python-to-Java (P2J) back-to-back code translation method, and associated tool called CoTran, based on large language models (LLMs). Our method leverages the attention mechanism of LLMs, compilation, and symbolic execution-based test generation for equivalence testing between the input and output programs. More precisely, we modify the typical LLM training loop to incorporate compiler and symbolic execution loss. Via extensive experiments comparing CoTran with 10 other transpilers and LLM-based translation tools over a benchmark of more than 57,000 Java-Python equivalent pairs, we show that CoTran outperforms them on relevant metrics such as compilation and runtime equivalence accuracy. For example, our tool gets 97.43% compilation accuracy and 49.66% runtime equivalence accuracy for J2P translation, whereas the nearest competing tool only gets 96.44% and 6.8% respectively.

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

Recent advances in Large Language Models (LLMs) have enabled researchers to focus on practical repository-level tasks in software engineering domain. In this work, we consider a cornerstone task for automating work with software repositories-environment setup, i.e., a task of configuring a repository-specific development environment on a system. Existing studies on environment setup introduce innovative agentic strategies, but their evaluation is often based on small datasets that may not capture the full range of configuration challenges encountered in practice. To address this gap, we introduce a comprehensive environment setup benchmark EnvBench. It encompasses 329 Python and 665 JVM-based (Java, Kotlin) repositories, with a focus on repositories that present genuine configuration challenges, excluding projects that can be fully configured by simple deterministic scripts. To enable further benchmark extension and usage for model tuning, we implement two automatic metrics: a static analysis check for missing imports in Python and a compilation check for JVM languages. We demonstrate the applicability of our benchmark by evaluating three environment setup approaches, including a simple zero-shot baseline and two agentic workflows, that we test with two powerful LLM backbones, GPT-4o and GPT-4o-mini. The best approach manages to successfully configure 6.69% repositories for Python and 29.47% repositories for JVM, suggesting that EnvBench remains challenging for current approaches. Our benchmark suite is publicly available at https://github.com/JetBrains-Research/EnvBench. The dataset and experiment trajectories are available at https://jb.gg/envbench.

Benchmarks play an important role in the development of machine learning algorithms. For example, research in reinforcement learning (RL) has been heavily influenced by available environments and benchmarks. However, RL environments are traditionally run on the CPU, limiting their scalability with typical academic compute. Recent advancements in JAX have enabled the wider use of hardware acceleration to overcome these computational hurdles, enabling massively parallel RL training pipelines and environments. This is particularly useful for multi-agent reinforcement learning (MARL) research. First of all, multiple agents must be considered at each environment step, adding computational burden, and secondly, the sample complexity is increased due to non-stationarity, decentralised partial observability, or other MARL challenges. In this paper, we present JaxMARL, the first open-source code base that combines ease-of-use with GPU enabled efficiency, and supports a large number of commonly used MARL environments as well as popular baseline algorithms. When considering wall clock time, our experiments show that per-run our JAX-based training pipeline is up to 12500x faster than existing approaches. This enables efficient and thorough evaluations, with the potential to alleviate the evaluation crisis of the field. We also introduce and benchmark SMAX, a vectorised, simplified version of the popular StarCraft Multi-Agent Challenge, which removes the need to run the StarCraft II game engine. This not only enables GPU acceleration, but also provides a more flexible MARL environment, unlocking the potential for self-play, meta-learning, and other future applications in MARL. We provide code at https://github.com/flairox/jaxmarl.

With the rise of software-as-a-service and microservice architectures, RESTful APIs are now ubiquitous in mobile and web applications. A service can have tens or hundreds of API methods, making it a challenge for programmers to find the right combination of methods to solve their task. We present APIphany, a component-based synthesizer for programs that compose calls to RESTful APIs. The main innovation behind APIphany is the use of precise semantic types, both to specify user intent and to direct the search. APIphany contributes three novel mechanisms to overcome challenges in adapting component-based synthesis to the REST domain: (1) a type inference algorithm for augmenting REST specifications with semantic types; (2) an efficient synthesis technique for "wrangling" semi-structured data, which is commonly required in working with RESTful APIs; and (3) a new form of simulated execution to avoid executing APIs calls during synthesis. We evaluate APIphany on three real-world APIs and 32 tasks extracted from GitHub repositories and StackOverflow. In our experiments, APIphany found correct solutions to 29 tasks, with 23 of them reported among top ten synthesis results.

In recent years, the application of large language models (LLMs) to code-related tasks has gained significant attention. However, existing evaluation benchmarks often focus on limited scenarios, such as code generation or completion, which do not reflect the diverse challenges developers face in real-world contexts. To address this, we introduce ComplexCodeEval, a benchmark designed to assess LCMs in various development tasks, including code generation, completion, API recommendation, and test case generation. It includes 3,897 Java samples and 7,184 Python samples from high-star GitHub repositories, each annotated with function signatures, docstrings, and API references to simulate real development environments. Our experiments across ten LCMs reveal that context improves performance and that data leakage can lead to overestimation, highlighting the need for more accurate evaluations.

Web API specifications are machine-readable descriptions of APIs. These specifications, in combination with related tooling, simplify and support the consumption of APIs. However, despite the increased distribution of web APIs, specifications are rare and their creation and maintenance heavily relies on manual efforts by third parties. In this paper, we propose an automatic approach and an associated tool called D2Spec for extracting specifications from web API documentation pages. Given a seed online documentation page on an API, D2Spec first crawls all documentation pages on the API, and then uses a set of machine learning techniques to extract the base URL, path templates, and HTTP methods, which collectively describe the endpoints of an API. We evaluated whether D2Spec can accurately extract endpoints from documentation on 120 web APIs. The results showed that D2Spec achieved a precision of 87.5% in identifying base URLs, a precision of 81.3% and a recall of 80.6% in generating path templates, and a precision of 84.4% and a recall of 76.2% in extracting HTTP methods. In addition, we found that D2Spec was useful when applied to APIs with pre-existing API specifications: D2Spec revealed many inconsistencies between web API documentation and their corresponding publicly available specifications. Thus, D2Spec can be used by web API providers to keep documentation and specifications in synchronization.

CLAX is a JAX-based library that implements classic click models using modern gradient-based optimization. While neural click models have emerged over the past decade, complex click models based on probabilistic graphical models (PGMs) have not systematically adopted gradient-based optimization, preventing practitioners from leveraging modern deep learning frameworks while preserving the interpretability of classic models. CLAX addresses this gap by replacing EM-based optimization with direct gradient-based optimization in a numerically stable manner. The framework's modular design enables the integration of any component, from embeddings and deep networks to custom modules, into classic click models for end-to-end optimization. We demonstrate CLAX's efficiency by running experiments on the full Baidu-ULTR dataset comprising over a billion user sessions in approx 2 hours on a single GPU, orders of magnitude faster than traditional EM approaches. CLAX implements ten classic click models, serving both industry practitioners seeking to understand user behavior and improve ranking performance at scale and researchers developing new click models. CLAX is available at: https://github.com/philipphager/clax

Human intelligence emerged through the process of natural selection and evolution on Earth. We investigate what it would take to re-create this process in silico. While past work has often focused on low-level processes (such as simulating physics or chemistry), we instead take a more targeted approach, aiming to evolve agents that can accumulate open-ended culture and technologies across generations. Towards this, we present JaxLife: an artificial life simulator in which embodied agents, parameterized by deep neural networks, must learn to survive in an expressive world containing programmable systems. First, we describe the environment and show that it can facilitate meaningful Turing-complete computation. We then analyze the evolved emergent agents' behavior, such as rudimentary communication protocols, agriculture, and tool use. Finally, we investigate how complexity scales with the amount of compute used. We believe JaxLife takes a step towards studying evolved behavior in more open-ended simulations. Our code is available at https://github.com/luchris429/JaxLife

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.

Recent breakthroughs in pre-trained code models, such as CodeBERT and Codex, have shown their superior performance in various downstream tasks. The correctness and unambiguity of API usage among these code models are crucial for achieving desirable program functionalities, requiring them to learn various API fully qualified names structurally and semantically. Recent studies reveal that even state-of-the-art pre-trained code models struggle with suggesting the correct APIs during code generation. However, the reasons for such poor API usage performance are barely investigated. To address this challenge, we propose using knowledge probing as a means of interpreting code models, which uses cloze-style tests to measure the knowledge stored in models. Our comprehensive study examines a code model's capability of understanding API fully qualified names from two different perspectives: API call and API import. Specifically, we reveal that current code models struggle with understanding API names, with pre-training strategies significantly affecting the quality of API name learning. We demonstrate that natural language context can assist code models in locating Python API names and generalize Python API name knowledge to unseen data. Our findings provide insights into the limitations and capabilities of current pre-trained code models, and suggest that incorporating API structure into the pre-training process can improve automated API usage and code representations. This work provides significance for advancing code intelligence practices and direction for future studies. All experiment results, data and source code used in this work are available at https://doi.org/10.5281/zenodo.7902072.

Retrieval-augmented generation (RAG) has increasingly shown its power in extending large language models' (LLMs') capability beyond their pre-trained knowledge. Existing works have shown that RAG can help with software development tasks such as code generation, code update, and test generation. Yet, the effectiveness of adapting LLMs to fast-evolving or less common API libraries using RAG remains unknown. To bridge this gap, we take an initial step to study this unexplored yet practical setting - when developers code with a less common library, they often refer to its API documentation; likewise, when LLMs are allowed to look up API documentation via RAG, to what extent can LLMs be advanced? To mimic such a setting, we select four less common open-source Python libraries with a total of 1017 eligible APIs. We study the factors that affect the effectiveness of using the documentation of less common API libraries as additional knowledge for retrieval and generation. Our intensive study yields interesting findings: (1) RAG helps improve LLMs' performance by 83%-220%. (2) Example code contributes the most to advance LLMs, instead of the descriptive texts and parameter lists in the API documentation. (3) LLMs could sometimes tolerate mild noises (typos in description or incorrect parameters) by referencing their pre-trained knowledge or document context. Finally, we suggest that developers pay more attention to the quality and diversity of the code examples in the API documentation. The study sheds light on future low-code software development workflows.

In recent years, the use of automated source code generation utilizing transformer-based generative models has expanded, and these models can generate functional code according to the requirements of the developers. However, recent research revealed that these automatically generated source codes can contain vulnerabilities and other quality issues. Despite researchers' and practitioners' attempts to enhance code generation models, retraining and fine-tuning large language models is time-consuming and resource-intensive. Thus, we describe FRANC, a lightweight framework for recommending more secure and high-quality source code derived from transformer-based code generation models. FRANC includes a static filter to make the generated code compilable with heuristics and a quality-aware ranker to sort the code snippets based on a quality score. Moreover, the framework uses prompt engineering to fix persistent quality issues. We evaluated the framework with five Python and Java code generation models and six prompt datasets, including a newly created one in this work (SOEval). The static filter improves 9% to 46% Java suggestions and 10% to 43% Python suggestions regarding compilability. The average improvement over the NDCG@10 score for the ranking system is 0.0763, and the repairing techniques repair the highest 80% of prompts. FRANC takes, on average, 1.98 seconds for Java; for Python, it takes 0.08 seconds.

The development of deep learning software libraries enabled significant progress in the field by allowing users to focus on modeling, while letting the library to take care of the tedious and time-consuming task of optimizing execution for modern hardware accelerators. However, this has benefited only particular types of deep learning models, such as Transformers, whose primitives map easily to the vectorized computation. The models that explicitly account for structured objects, such as trees and segmentations, did not benefit equally because they require custom algorithms that are difficult to implement in a vectorized form. SynJax directly addresses this problem by providing an efficient vectorized implementation of inference algorithms for structured distributions covering alignment, tagging, segmentation, constituency trees and spanning trees. With SynJax we can build large-scale differentiable models that explicitly model structure in the data. The code is available at https://github.com/deepmind/synjax.

Code generation models based on the pre-training and fine-tuning paradigm have been increasingly attempted by both academia and industry, resulting in well-known industrial models such as Codex, CodeGen, and PanGu-Coder. To evaluate the effectiveness of these models, multiple existing benchmarks are proposed, including only cases of generating a standalone function, i.e., a function that may invoke or access only built-in functions and standard libraries. However, non-standalone functions, which typically are not included in the existing benchmarks, constitute more than 70% of the functions in popular open-source projects, and evaluating models' effectiveness on standalone functions cannot reflect these models' effectiveness on pragmatic code generation scenarios. To help bridge the preceding gap, in this paper, we propose a benchmark named CoderEval, consisting of 230 Python and 230 Java code generation tasks carefully curated from popular real-world open-source projects and a self-contained execution platform to automatically assess the functional correctness of generated code. CoderEval supports code generation tasks from six levels of context dependency, where context refers to code elements such as types, APIs, variables, and consts defined outside the function under generation but within the dependent third-party libraries, current class, file, or project. CoderEval can be used to evaluate the effectiveness of models in generating code beyond only standalone functions. By evaluating three code generation models on CoderEval, we find that the effectiveness of these models in generating standalone functions is substantially higher than that in generating non-standalone functions. Our analysis highlights the current progress and pinpoints future directions to further improve a model's effectiveness by leveraging contextual information for pragmatic code generation.

Machine Learning Interatomic Potentials (MLIP) are a novel in silico approach for molecular property prediction, creating an alternative to disrupt the accuracy/speed trade-off of empirical force fields and density functional theory (DFT). In this white paper, we present our MLIP library which was created with two core aims: (1) provide to industry experts without machine learning background a user-friendly and computationally efficient set of tools to experiment with MLIP models, (2) provide machine learning developers a framework to develop novel approaches fully integrated with molecular dynamics tools. The library includes in this release three model architectures (MACE, NequIP, and ViSNet), and two molecular dynamics (MD) wrappers (ASE, and JAX-MD), along with a set of pre-trained organics models. The seamless integration with JAX-MD, in particular, facilitates highly efficient MD simulations, bringing MLIP models significantly closer to industrial application. The library is available on GitHub and on PyPI under the Apache license 2.0.

Large language models (LLMs), such as Codex and GPT-4, have recently showcased their remarkable code generation abilities, facilitating a significant boost in coding efficiency. This paper will delve into utilizing LLMs for code generation in private libraries, as they are widely employed in everyday programming. Despite their remarkable capabilities, generating such private APIs poses a formidable conundrum for LLMs, as they inherently lack exposure to these private libraries during pre-training. To address this challenge, we propose a novel framework that emulates the process of programmers writing private code. This framework comprises two modules: APIFinder first retrieves potentially useful APIs from API documentation; and APICoder then leverages these retrieved APIs to generate private code. Specifically, APIFinder employs vector retrieval techniques and allows user involvement in the retrieval process. For APICoder, it can directly utilize off-the-shelf code generation models. To further cultivate explicit proficiency in invoking APIs from prompts, we continuously pre-train a reinforced version of APICoder, named CodeGenAPI. Our goal is to train the above two modules on vast public libraries, enabling generalization to private ones. Meanwhile, we create four private library benchmarks, including TorchDataEval, TorchDataComplexEval, MonkeyEval, and BeatNumEval, and meticulously handcraft test cases for each benchmark to support comprehensive evaluations. Numerous experiments on the four benchmarks consistently affirm the effectiveness of our approach. Furthermore, deeper analysis is also conducted to glean additional insights.

The rapid evolution of software libraries presents a significant challenge for code generation models, which must adapt to frequent version updates while maintaining compatibility with previous versions. Existing code completion benchmarks often overlook this dynamic aspect, and the one that does consider it relies on static code prediction tasks without execution-based evaluation, offering a limited perspective on a model's practical usability. To address this gap, we introduce \GitChameleon{}, a novel, manually curated dataset comprising 116 Python code completion problems, each conditioned on specific library versions and accompanied by executable unit tests. is designed to rigorously assess the ability of modern large language models (LLMs) to generate version-specific code that is not only syntactically correct but also functionally accurate upon execution. Our comprehensive evaluations reveal that state-of-the-art LLMs struggle with this task; for instance, GPT-4o achieves a pass@10 of only 39.9\% (43.7\% when provided with error feedback), highlighting the complexity of the problem and the limitations of current models. By providing an execution-based benchmark that emphasizes the dynamic nature of code libraries, serves as a critical tool to advance the development of more adaptable and reliable code generation models. For facilitation for further exploration of version-conditioned code generation, we make our code repository publicly accessible at https://github.com/NizarIslah/GitChameleon.

Large Language Models (LLMs) have shown promise in automated code generation but typically excel only in simpler tasks such as generating standalone code units. Real-world software development, however, often involves complex code repositories (named repo) with complex dependencies and extensive documentation. To fill this gap, our research pivots towards evaluating LLMs in a more realistic setting -- real-world repo-level code generation. We introduce CodeAgentBench, a manually curated benchmark for repo-level code generation. This benchmark comprises five high-quality Python projects, encompassing a total of 101 samples. We assess nine leading LLMs on repo-level tasks and observe a decline in their performance. To tackle this, we present CodeAgent, a novel LLM-based agent framework that employs external tools for effective repo-level code generation. CodeAgent integrates five programming tools, enabling interaction with software artifacts for information retrieval, code symbol navigation, and code testing. We implement four agent strategies to optimize these tools' usage. Our experiments on CodeAgentBench show that CodeAgent enhances LLM performance significantly, with improvements ranging from 18.1\% to 250\%. Further tests on the HumanEval benchmark confirm CodeAgent's adaptability and efficacy across various code generation tasks. Notably, CodeAgent outperforms commercial products like Github Copilot, showcasing superior accuracy and efficiency. These results demonstrate CodeAgent's robust capabilities in code generation, highlighting its potential for real-world repo-level coding challenges.

LLMs have demonstrated significant potential in code generation tasks, achieving promising results at the function or statement level across various benchmarks. However, the complexities associated with creating code artifacts like classes, particularly within the context of real-world software repositories, remain underexplored. Prior research treats class-level generation as an isolated task, neglecting the intricate dependencies & interactions that characterize real-world software environments. To address this gap, we introduce RepoClassBench, a comprehensive benchmark designed to rigorously evaluate LLMs in generating complex, class-level code within real-world repositories. RepoClassBench includes "Natural Language to Class generation" tasks across Java, Python & C# from a selection of repositories. We ensure that each class in our dataset not only has cross-file dependencies within the repository but also includes corresponding test cases to verify its functionality. We find that current models struggle with the realistic challenges posed by our benchmark, primarily due to their limited exposure to relevant repository contexts. To address this shortcoming, we introduce Retrieve-Repotools-Reflect (RRR), a novel approach that equips LLMs with static analysis tools to iteratively navigate & reason about repository-level context in an agent-based framework. Our experiments demonstrate that RRR significantly outperforms existing baselines on RepoClassBench, showcasing its effectiveness across programming languages & under various settings. Our findings emphasize the critical need for code-generation benchmarks to incorporate repo-level dependencies to more accurately reflect the complexities of software development. Our work shows the benefits of leveraging specialized tools to enhance LLMs' understanding of repository context. We plan to make our dataset & evaluation harness public.

This paper presents NT-Java-1.1B, an open-source specialized code language model built on StarCoderBase-1.1B, designed for coding tasks in Java programming. NT-Java-1.1B achieves state-of-the-art performance, surpassing its base model and majority of other models of similar size on MultiPL-E Java code benchmark. While there have been studies on extending large, generic pre-trained models to improve proficiency in specific programming languages like Python, similar investigations on small code models for other programming languages are lacking. Large code models require specialized hardware like GPUs for inference, highlighting the need for research into building small code models that can be deployed on developer desktops. This paper addresses this research gap by focusing on the development of a small Java code model, NT-Java-1.1B, and its quantized versions, which performs comparably to open models around 1.1B on MultiPL-E Java code benchmarks, making them ideal for desktop deployment. This paper establishes the foundation for specialized models across languages and sizes for a family of NT Models.

With the growing reliance on automated code completion tools in software development, the need for robust evaluation benchmarks has become critical. However, existing benchmarks focus more on code generation tasks in function and class level and provide rich text description to prompt the model. By contrast, such descriptive prompt is commonly unavailable in real development and code completion can occur in wider range of situations such as in the middle of a function or a code block. These limitations makes the evaluation poorly align with the practical scenarios of code completion tools. In this paper, we propose RepoMasterEval, a novel benchmark for evaluating code completion models constructed from real-world Python and TypeScript repositories. Each benchmark datum is generated by masking a code snippet (ground truth) from one source code file with existing test suites. To improve test accuracy of model generated code, we employ mutation testing to measure the effectiveness of the test cases and we manually crafted new test cases for those test suites with low mutation score. Our empirical evaluation on 6 state-of-the-art models shows that test argumentation is critical in improving the accuracy of the benchmark and RepoMasterEval is able to report difference in model performance in real-world scenarios. The deployment of RepoMasterEval in a collaborated company for one month also revealed that the benchmark is useful to give accurate feedback during model training and the score is in high correlation with the model's performance in practice. Based on our findings, we call for the software engineering community to build more LLM benchmarks tailored for code generation tools taking the practical and complex development environment into consideration.

Code completion aims to help improve developers' productivity by suggesting the next code tokens from a given context. Various approaches have been proposed to incorporate abstract syntax tree (AST) information for model training, ensuring that code completion is aware of the syntax of the programming languages. However, existing syntax-aware code completion approaches are not on-the-fly, as we found that for every two-thirds of characters that developers type, AST fails to be extracted because it requires the syntactically correct source code, limiting its practicality in real-world scenarios. On the other hand, existing on-the-fly code completion does not consider syntactic information yet. In this paper, we propose PyCoder to leverage token types, a kind of lightweight syntactic information, which is readily available and aligns with the natural order of source code. Our PyCoder is trained in a multi-task training manner so that by learning the supporting task of predicting token types during the training phase, the models achieve better performance on predicting tokens and lines of code without the need for token types in the inference phase. Comprehensive experiments show that PyCoder achieves the first rank on the CodeXGLUE leaderboard with an accuracy of 77.12% for the token-level predictions, which is 0.43%-24.25% more accurate than baselines. In addition, PyCoder achieves an exact match of 43.37% for the line-level predictions, which is 3.63%-84.73% more accurate than baselines. These results lead us to conclude that token type information (an alternative to syntactic information) that is rarely used in the past can greatly improve the performance of code completion approaches, without requiring the syntactically correct source code like AST-based approaches do. Our PyCoder is publicly available on HuggingFace.

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.

Automated code review (CR) is a key application for Large Language Models (LLMs), but progress is hampered by a "reality gap": existing benchmarks evaluate models on isolated sub-tasks using simplified, context-poor data. This fails to reflect the holistic context-rich nature of real-world CR. To bridge this gap, we introduce CodeFuse-CR-Bench, the first comprehensiveness-aware benchmark for repository-level CR evaluation. CodeFuse-CR-Bench comprises 601 high-quality instances from 70 Python projects covering nine Pull-Request (PR) problem domains, where each instance provides rich, multi-faceted context including the associated issue, PR details, and repository state, enabling end-to-end evaluation. Beyond superficial metrics, we also propose a novel evaluation framework that combines rule-based checks for location and syntax with model-based judgments of review quality. We present the first large-scale assessment of state-of-the-art LLMs on this comprehensive CR task. Our results establish crucial baselines and reveal that (1) no single LLM dominates all aspects of CR; (2) Gemini 2.5 Pro achieves the highest comprehensive performance; and (3) different LLMs exhibit varying robustness to redundant context. These findings highlight the necessity of holistic, multi-dimensional evaluation and provide actionable insights for advancing truly intelligent yet practical CR assistants.

A package's source code repository records the development history of the package, providing indispensable information for the use and risk monitoring of the package. However, a package release often misses its source code repository due to the separation of the package's development platform from its distribution platform. Existing tools retrieve the release's repository information from its metadata, which suffers from two limitations: the metadata may not contain or contain wrong information. Our analysis shows that existing tools can only retrieve repository information for up to 70.5% of PyPI releases. To address the limitations, this paper proposes PyRadar, a novel framework that utilizes the metadata and source distribution to retrieve and validate the repository information for PyPI releases. We start with an empirical study to compare four existing tools on 4,227,425 PyPI releases and analyze phantom files (files appearing in the release's distribution but not in the release's repository) in 14,375 correct package-repository links and 2,064 incorrect links. Based on the findings, we design PyRadar with three components, i.e., Metadata-based Retriever, Source Code Repository Validator, and Source Code-based Retriever. In particular, the Metadata-based Retriever combines best practices of existing tools and successfully retrieves repository information from the metadata for 72.1% of PyPI releases. The Source Code Repository Validator applies common machine learning algorithms on six crafted features and achieves an AUC of up to 0.995. The Source Code-based Retriever queries World of Code with the SHA-1 hashes of all Python files in the release's source distribution and retrieves repository information for 90.2% of packages in our dataset with an accuracy of 0.970. Both practitioners and researchers can employ the PyRadar to better use PyPI packages.

The task of repository-level code completion is to continue writing the unfinished code based on a broader context of the repository. While for automated code completion tools, it is difficult to utilize the useful information scattered in different files. We propose RepoCoder, a simple, generic, and effective framework to address the challenge. It streamlines the repository-level code completion process by incorporating a similarity-based retriever and a pre-trained code language model in an iterative retrieval-generation pipeline. RepoCoder makes effective utilization of repository-level information for code completion and has the ability to generate code at various levels of granularity. Moreover, we propose a new benchmark RepoEval, which consists of the latest and high-quality real-world repositories covering line, API invocation, and function body completion scenarios. Experimental results indicate that RepoCoder significantly improves the In-File completion baseline by over 10% in all settings and consistently outperforms the vanilla retrieval-augmented code completion approach. Furthermore, we validate the effectiveness of RepoCoder through comprehensive analysis, providing valuable insights for future research. Our source code and benchmark are publicly available: https://github.com/microsoft/CodeT/tree/main/RepoCoder

Foundation models for materials modeling are advancing quickly, but their training remains expensive, often placing state-of-the-art methods out of reach for many research groups. We introduce Nequix, a compact E(3)-equivariant potential that pairs a simplified NequIP design with modern training practices, including equivariant root-mean-square layer normalization and the Muon optimizer, to retain accuracy while substantially reducing compute requirements. Built in JAX, Nequix has 700K parameters and was trained in 500 A100-GPU hours. On the Matbench-Discovery and MDR Phonon benchmarks, Nequix ranks third overall while requiring less than one quarter of the training cost of most other methods, and it delivers an order-of-magnitude faster inference speed than the current top-ranked model. We release model weights and fully reproducible codebase at https://github.com/atomicarchitects/nequix

The rapid evolution of software libraries poses a considerable hurdle for code generation, necessitating continuous adaptation to frequent version updates while preserving backward compatibility. While existing code evolution benchmarks provide valuable insights, they typically lack execution-based evaluation for generating code compliant with specific library versions. To address this, we introduce GitChameleon, a novel, meticulously curated dataset comprising 328 Python code completion problems, each conditioned on specific library versions and accompanied by executable unit tests. GitChameleon rigorously evaluates the capacity of contemporary large language models (LLMs), LLM-powered agents, code assistants, and RAG systems to perform version-conditioned code generation that demonstrates functional accuracy through execution. Our extensive evaluations indicate that state-of-the-art systems encounter significant challenges with this task; enterprise models achieving baseline success rates in the 48-51\% range, underscoring the intricacy of the problem. By offering an execution-based benchmark emphasizing the dynamic nature of code libraries, GitChameleon enables a clearer understanding of this challenge and helps guide the development of more adaptable and dependable AI code generation methods. We make the dataset and evaluation code publicly available at https://github.com/mrcabbage972/GitChameleonBenchmark.

Recent advancements in large language models (LLMs) have demonstrated promising capabilities in code generation tasks. However, most existing benchmarks focus on isolated functions and fail to capture the complexity of real-world, class-level software structures. To address this gap, we introduce a large-scale, Python class-level dataset curated from 13{,}174 real-world open-source projects. The dataset contains over 842,000 class skeletons, each including class and method signatures, along with associated docstrings when available. We preserve structural and contextual dependencies critical to realistic software development scenarios and enrich the dataset with static code metrics to support downstream analysis. To evaluate the usefulness of this dataset, we use extracted class skeletons as prompts for GPT-4 to generate full class implementations. Results show that the LLM-generated classes exhibit strong lexical and structural similarity to human-written counterparts, with average ROUGE@L, BLEU, and TSED scores of 0.80, 0.59, and 0.73, respectively. These findings confirm that well-structured prompts derived from real-world class skeletons significantly enhance LLM performance in class-level code generation. This dataset offers a valuable resource for benchmarking, training, and improving LLMs in realistic software engineering contexts.

The recently introduced Mojo programming language (PL) by Modular, has received significant attention in the scientific community due to its claimed significant speed boost over Python. Despite advancements in code Large Language Models (LLMs) across various PLs, Mojo remains unexplored in this context. To address this gap, we introduce MojoBench, the first framework for Mojo code generation. MojoBench includes HumanEval-Mojo, a benchmark dataset designed for evaluating code LLMs on Mojo, and Mojo-Coder, the first LLM pretrained and finetuned for Mojo code generation, which supports instructions in 5 natural languages (NLs). Our results show that Mojo-Coder achieves a 30-35% performance improvement over leading models like GPT-4o and Claude-3.5-Sonnet. Furthermore, we provide insights into LLM behavior with underrepresented and unseen PLs, offering potential strategies for enhancing model adaptability. MojoBench contributes to our understanding of LLM capabilities and limitations in emerging programming paradigms fostering more robust code generation systems.

Tests that cause spurious failures without any code changes, i.e., flaky tests, hamper regression testing, increase maintenance costs, may shadow real bugs, and decrease trust in tests. While the prevalence and importance of flakiness is well established, prior research focused on Java projects, thus raising the question of how the findings generalize. In order to provide a better understanding of the role of flakiness in software development beyond Java, we empirically study the prevalence, causes, and degree of flakiness within software written in Python, one of the currently most popular programming languages. For this, we sampled 22352 open source projects from the popular PyPI package index, and analyzed their 876186 test cases for flakiness. Our investigation suggests that flakiness is equally prevalent in Python as it is in Java. The reasons, however, are different: Order dependency is a much more dominant problem in Python, causing 59% of the 7571 flaky tests in our dataset. Another 28% were caused by test infrastructure problems, which represent a previously undocumented cause of flakiness. The remaining 13% can mostly be attributed to the use of network and randomness APIs by the projects, which is indicative of the type of software commonly written in Python. Our data also suggests that finding flaky tests requires more runs than are often done in the literature: A 95% confidence that a passing test case is not flaky on average would require 170 reruns.

OpenAI's Codex, a GPT-3 like model trained on a large code corpus, has made headlines in and outside of academia. Given a short user-provided description, it is capable of synthesizing code snippets that are syntactically and semantically valid in most cases. In this work, we want to investigate whether Codex is able to localize and fix bugs, a task of central interest in the field of automated program repair. Our initial evaluation uses the multi-language QuixBugs benchmark (40 bugs in both Python and Java). We find that, despite not being trained for APR, Codex is surprisingly effective, and competitive with recent state of the art techniques. Our results also show that Codex is slightly more successful at repairing Python than Java.

The fastrerandomize R package provides hardware-accelerated tools for performing rerandomization and randomization testing in experimental research. Using a JAX backend, the package enables exact rerandomization inference even for large experiments with hundreds of billions of possible randomizations. Key functionalities include generating pools of acceptable rerandomizations based on covariate balance, conducting exact randomization tests, and performing pre-analysis evaluations to determine optimal rerandomization acceptance thresholds. Through batched processing and GPU acceleration, fastrerandomize achieves substantial performance gains compared to existing implementations, making previously intractable designs computationally feasible. The package therefore extends the randomization-based inference toolkit in R, allowing researchers to efficiently implement more stringent rerandomization designs and conduct valid inference even with large sample sizes or in high-dimensional settings.

The application of machine learning algorithms to source code has grown in the past years. Since these algorithms are quite sensitive to input data, it is not surprising that researchers experiment with input representations. Nowadays, a popular starting point to represent code is abstract syntax trees (ASTs). Abstract syntax trees have been used for a long time in various software engineering domains, and in particular in IDEs. The API of modern IDEs allows to manipulate and traverse ASTs, resolve references between code elements, etc. Such algorithms can enrich ASTs with new data and therefore may be useful in ML-based code analysis. In this work, we present PSIMiner - a tool for processing PSI trees from the IntelliJ Platform. PSI trees contain code syntax trees as well as functions to work with them, and therefore can be used to enrich code representation using static analysis algorithms of modern IDEs. To showcase this idea, we use our tool to infer types of identifiers in Java ASTs and extend the code2seq model for the method name prediction problem.

Pretrained code language models have enabled great progress towards program synthesis. However, common approaches only consider in-file local context and thus miss information and constraints imposed by other parts of the codebase and its external dependencies. Existing code completion benchmarks also lack such context. To resolve these restrictions we curate a new dataset of permissively licensed Python packages that includes full projects and their dependencies and provide tools to extract non-local information with the help of program analyzers. We then focus on the task of function call argument completion which requires predicting the arguments to function calls. We show that existing code completion models do not yield good results on our completion task. To better solve this task, we query a program analyzer for information relevant to a given function call, and consider ways to provide the analyzer results to different code completion models during inference and training. Our experiments show that providing access to the function implementation and function usages greatly improves the argument completion performance. Our ablation study provides further insights on how different types of information available from the program analyzer and different ways of incorporating the information affect the model performance.

AlphaFold predicts protein structures from the amino acid sequence at or near experimental resolution, solving the 50-year-old protein folding challenge, leading to progress by transforming large-scale genomics data into protein structures. AlphaFold will also greatly change the scientific research model from low-throughput to high-throughput manner. The AlphaFold framework is a mixture of two types of workloads: MSA construction based on CPUs and model inference on GPUs. The first CPU stage dominates the overall runtime, taking hours for a single protein due to the large database sizes and I/O bottlenecks. However, GPUs in this CPU stage remain idle, resulting in low GPU utilization and restricting the capacity of large-scale structure predictions. Therefore, we proposed ParaFold, an open-source parallel version of AlphaFold for high throughput protein structure predictions. ParaFold separates the CPU and GPU parts to enable large-scale structure predictions. ParaFold also effectively reduces the CPU and GPU runtime with two optimizations without compromising the quality of prediction results: using multi-threaded parallelism on CPUs and using optimized JAX compilation on GPUs. We evaluated ParaFold with three datasets of different size and protein lengths. We evaluated the accuracy and efficiency of optimizations on CPUs and GPUs, and showed the large-scale prediction capability by running ParaFold inferences of 19,704 small proteins in five hours on one NVIDIA DGX-2. Using the JAX compile optimization, ParaFold attained a 13.8X average speedup over AlphaFold. ParaFold offers a rapid and effective approach for high-throughput structure predictions, leveraging the predictive power by running on supercomputers, with shorter time, and at a lower cost. The development of ParaFold will greatly speed up high-throughput studies and render the protein "structure-omics" feasible.

Advancing automated programming necessitates robust and comprehensive code generation benchmarks, yet current evaluation frameworks largely neglect object-oriented programming (OOP) in favor of functional programming (FP), e.g., HumanEval and MBPP. To address this, our study introduces a pioneering OOP-focused benchmark, featuring 431 Python programs that encompass essential OOP concepts and features like classes and encapsulation methods. We propose a novel evaluation metric, pass@o, tailored for OOP, enhancing traditional pass@k measures. Our evaluation of 23 leading large language models (LLMs), including both general and code-specialized models, reveals three key insights: 1) pass@o offers a more relevant and comprehensive assessment for OOP code generation; 2) Despite excelling in FP, code-specialized LLMs like WizardCoder lag in OOP compared to models like ChatGPT; 3) The poor performance of all advanced LLMs on our OOP benchmark highlights a critical need for improvements in this field. Our benchmark and scripts are publicly released at: https://github.com/alphadl/OOP-eval.

Implementing automated unit tests is an important but time-consuming activity in software development. To assist developers in this task, many techniques for automating unit test generation have been developed. However, despite this effort, usable tools exist for very few programming languages. Moreover, studies have found that automatically generated tests suffer poor readability and do not resemble developer-written tests. In this work, we present a rigorous investigation of how large language models (LLMs) can help bridge the gap. We describe a generic pipeline that incorporates static analysis to guide LLMs in generating compilable and high-coverage test cases. We illustrate how the pipeline can be applied to different programming languages, specifically Java and Python, and to complex software requiring environment mocking. We conducted an empirical study to assess the quality of the generated tests in terms of code coverage and test naturalness -- evaluating them on standard as well as enterprise Java applications and a large Python benchmark. Our results demonstrate that LLM-based test generation, when guided by static analysis, can be competitive with, and even outperform, state-of-the-art test-generation techniques in coverage achieved while also producing considerably more natural test cases that developers find easy to understand. We also present the results of a user study, conducted with 161 professional developers, that highlights the naturalness characteristics of the tests generated by our approach.

We introduce DS-1000, a code generation benchmark with a thousand data science problems spanning seven Python libraries, such as NumPy and Pandas. Compared to prior works, DS-1000 incorporates three core features. First, our problems reflect diverse, realistic, and practical use cases since we collected them from StackOverflow. Second, our automatic evaluation is highly specific (reliable) -- across all Codex-002-predicted solutions that our evaluation accept, only 1.8% of them are incorrect; we achieve this with multi-criteria metrics, checking both functional correctness by running test cases and surface-form constraints by restricting API usages or keywords. Finally, we proactively defend against memorization by slightly modifying our problems to be different from the original StackOverflow source; consequently, models cannot answer them correctly by memorizing the solutions from pre-training. The current best public system (Codex-002) achieves 43.3% accuracy, leaving ample room for improvement. We release our benchmark at https://ds1000-code-gen.github.io.

Large language models have demonstrated the ability to generate both natural language and programming language text. Such models open up the possibility of multi-language code generation: could code generation models generalize knowledge from one language to another? Although contemporary code generation models can generate semantically correct Python code, little is known about their abilities with other languages. We propose MultiPL-E, a system for translating unit test-driven code generation benchmarks to new languages. We create the first massively multilingual code generation benchmark by using MultiPL-E to translate two popular Python code generation benchmarks to 18 additional programming languages. We use MultiPL-E to extend the HumanEval benchmark and MBPP benchmark to 18 languages that encompass a range of programming paradigms and popularity. Using these new parallel benchmarks, we evaluate the multi-language performance of three state-of-the-art code generation models: Codex, CodeGen, and InCoder. We find that Codex matches or even exceeds its performance on Python for several other languages. The range of programming languages represented in MultiPL-E allow us to explore the impact of language frequency and language features on model performance. Finally, the MultiPL-E approach of compiling code generation benchmarks to new programming languages is both scalable and extensible, making it straightforward to evaluate new models, benchmarks, and languages.

Large language models trained on code have shown great potential to increase productivity of software developers. Several execution-based benchmarks have been proposed to evaluate functional correctness of model-generated code on simple programming problems. Nevertheless, it is expensive to perform the same evaluation on complex real-world projects considering the execution cost. On the contrary, static analysis tools such as linters, which can detect errors without running the program, haven't been well explored for evaluating code generation models. In this work, we propose a static evaluation framework to quantify static errors in Python code completions, by leveraging Abstract Syntax Trees. Compared with execution-based evaluation, our method is not only more efficient, but also applicable to code in the wild. For experiments, we collect code context from open source repos to generate one million function bodies using public models. Our static analysis reveals that Undefined Name and Unused Variable are the most common errors among others made by language models. Through extensive studies, we also show the impact of sampling temperature, model size, and context on static errors in code completions.

We introduce Codex, a GPT language model fine-tuned on publicly available code from GitHub, and study its Python code-writing capabilities. A distinct production version of Codex powers GitHub Copilot. On HumanEval, a new evaluation set we release to measure functional correctness for synthesizing programs from docstrings, our model solves 28.8% of the problems, while GPT-3 solves 0% and GPT-J solves 11.4%. Furthermore, we find that repeated sampling from the model is a surprisingly effective strategy for producing working solutions to difficult prompts. Using this method, we solve 70.2% of our problems with 100 samples per problem. Careful investigation of our model reveals its limitations, including difficulty with docstrings describing long chains of operations and with binding operations to variables. Finally, we discuss the potential broader impacts of deploying powerful code generation technologies, covering safety, security, and economics.

This paper presents BPMN Assistant, a tool that leverages Large Language Models (LLMs) for natural language-based creation and editing of BPMN diagrams. A specialized JSON-based representation is introduced as a structured alternative to the direct handling of XML to enhance the accuracy of process modifications. Process generation quality is evaluated using Graph Edit Distance (GED) and Relative Graph Edit Distance (RGED), while editing performance is evaluated with a binary success metric. Results show that JSON and XML achieve similar similarity scores in generation, but JSON offers greater reliability, faster processing, and significantly higher editing success rates. We discuss key trade-offs, limitations, and future improvements. The implementation is available at https://github.com/jtlicardo/bpmn-assistant.

Context: Jupyter Notebook has emerged as a versatile tool that transforms how researchers, developers, and data scientists conduct and communicate their work. As the adoption of Jupyter notebooks continues to rise, so does the interest from the software engineering research community in improving the software engineering practices for Jupyter notebooks. Objective: The purpose of this study is to analyze trends, gaps, and methodologies used in software engineering research on Jupyter notebooks. Method: We selected 146 relevant publications from the DBLP Computer Science Bibliography up to the end of 2024, following established systematic literature review guidelines. We explored publication trends, categorized them based on software engineering topics, and reported findings based on those topics. Results: The most popular venues for publishing software engineering research on Jupyter notebooks are related to human-computer interaction instead of traditional software engineering venues. Researchers have addressed a wide range of software engineering topics on notebooks, such as code reuse, readability, and execution environment. Although reusability is one of the research topics for Jupyter notebooks, only 64 of the 146 studies can be reused based on their provided URLs. Additionally, most replication packages are not hosted on permanent repositories for long-term availability and adherence to open science principles. Conclusion: Solutions specific to notebooks for software engineering issues, including testing, refactoring, and documentation, are underexplored. Future research opportunities exist in automatic testing frameworks, refactoring clones between notebooks, and generating group documentation for coherent code cells.

Retrieval Augmented Generation (RAG) has emerged as a standard paradigm for enhancing the factual accuracy and contextual relevance of Large Language Models (LLMs) by integrating retrieval mechanisms. However, existing evaluation frameworks fail to provide a holistic black-box approach to assessing RAG systems, especially in real-world deployment scenarios. To address this gap, we introduce SCARF (System for Comprehensive Assessment of RAG Frameworks), a modular and flexible evaluation framework designed to benchmark deployed RAG applications systematically. SCARF provides an end-to-end, black-box evaluation methodology, enabling a limited-effort comparison across diverse RAG frameworks. Our framework supports multiple deployment configurations and facilitates automated testing across vector databases and LLM serving strategies, producing a detailed performance report. Moreover, SCARF integrates practical considerations such as response coherence, providing a scalable and adaptable solution for researchers and industry professionals evaluating RAG applications. Using the REST APIs interface, we demonstrate how SCARF can be applied to real-world scenarios, showcasing its flexibility in assessing different RAG frameworks and configurations. SCARF is available at GitHub repository.

In the rapidly evolving software development landscape, Python stands out for its simplicity, versatility, and extensive ecosystem. Python packages, as units of organization, reusability, and distribution, have become a pressing concern, highlighted by the considerable number of vulnerability reports. As a scripting language, Python often cooperates with other languages for performance or interoperability. This adds complexity to the vulnerabilities inherent to Python packages, and the effectiveness of current vulnerability detection tools remains underexplored. This paper addresses these gaps by introducing PyVul, the first comprehensive benchmark suite of Python-package vulnerabilities. PyVul includes 1,157 publicly reported, developer-verified vulnerabilities, each linked to its affected packages. To accommodate diverse detection techniques, it provides annotations at both commit and function levels. An LLM-assisted data cleansing method is incorporated to improve label accuracy, achieving 100% commit-level and 94% function-level accuracy, establishing PyVul as the most precise large-scale Python vulnerability benchmark. We further carry out a distribution analysis of PyVul, which demonstrates that vulnerabilities in Python packages involve multiple programming languages and exhibit a wide variety of types. Moreover, our analysis reveals that multi-lingual Python packages are potentially more susceptible to vulnerabilities. Evaluation of state-of-the-art detectors using this benchmark reveals a significant discrepancy between the capabilities of existing tools and the demands of effectively identifying real-world security issues in Python packages. Additionally, we conduct an empirical review of the top-ranked CWEs observed in Python packages, to diagnose the fine-grained limitations of current detection tools and highlight the necessity for future advancements in the field.

Code generation benchmarks such as HumanEval are widely adopted to evaluate LLMs' capabilities. However, after consolidating the latest 24 benchmarks, we noticed three significant imbalances. First, imbalanced programming language. 95.8% of benchmarks involve Python, while only 5 benchmarks involve Java. Second, imbalanced code granularity. Function-/statement-level benchmarks account for over 83.3% of benchmarks. Only a mere handful extends to class-/project-levels, and all are limited to Python. Third, lacking advanced features. Existing benchmarks primarily assess basic coding skills, while overlooking advanced Object-Oriented Programming (OOP) features (i.e., encapsulation, inheritance, and polymorphism). To fill these gaps, we propose JavaBench, a project-level Java benchmark that exercises OOP features. It comprises four Java projects with 389 methods in 106 Java classes. The test coverage is up to 92%, and JavaBench is attested by 282 undergraduate students, reaching a 90.93/100 average score (i.e., pass rate against the test suite), ensuring the quality of documentation, code skeleton, and tests. To better evaluate LLM's capability against JavaBench, we introduce a systematic evaluation design covering three context settings and five synthesis strategies at two granularities using three hierarchical metrics. Our extensive experiment yields several interesting findings. First, we noticed that regarding project-level Java programming, LLMs are far behind undergraduate students (no project can be correctly completed by any studied LLMs, and at most 41.17% Pass@5 in a more relaxed evaluation). Second, using method signature as prompt context may strike an ideal balance for project-level code generation. JavaBench is publicly available at https://github.com/java-bench/JavaBench.

Large language models have made substantial progress in addressing diverse code-related tasks. However, their adoption is hindered by inconsistencies in generating output due to the lack of real-world, domain-specific information, such as for intra-repository API calls for unseen software projects. We introduce a novel technique to mitigate hallucinations by leveraging global and local contextual information within a code repository for API completion tasks. Our approach is tailored to refine code completion tasks, with a focus on optimizing local API completions. We examine relevant import statements during API completion to derive insights into local APIs, drawing from their method signatures. For API token completion, we analyze the inline variables and correlate them with the appropriate imported modules, thereby allowing our approach to rank the most contextually relevant suggestions from the available local APIs. Further, for conversational API completion, we gather APIs that are most relevant to the developer query with a retrieval-based search across the project. We employ our tool, LANCE, within the framework of our proposed benchmark, APIEval, encompassing two different programming languages. Our evaluation yields an average accuracy of 82.6% for API token completion and 76.9% for conversational API completion tasks. On average, LANCE surpasses Copilot by 143% and 142% for API token completion and conversational API completion, respectively. The implications of our findings are substantial for developers, suggesting that our lightweight context analysis can be applied to multilingual environments without language-specific training or fine-tuning, allowing for efficient implementation with minimal examples and effort.

In the evolving landscape of software development, Large Language Models (LLMs) exhibit a unique phenomenon known as emergent abilities, demonstrating adeptness across numerous tasks, from text summarization to code generation. While these abilities open up novel avenues in software design and crafting, their incorporation presents substantial challenges. Developers grapple with decisions surrounding the direct embedding of LLMs within applications versus employing them for code generation. Moreover, effective prompt design becomes a critical concern, given the necessity of data extraction from natural language outputs. To address these intricacies, this paper introduces AskIt, a domain-specific language (DSL) specifically designed for LLMs. AskIt simplifies LLM integration, offering type-guided output control, template-based function definitions, and a unified interface that diminishes the distinction between LLM-based code generation and application integration. Furthermore, through Programming by Example (PBE), AskIt harnesses the power of few-shot learning at the programming language level. Our evaluations underscore AskIt's potency. Across 50 tasks, AskIt generated concise prompts for the given tasks, achieving a 16.14% reduction in prompt length relative to benchmarks. Additionally, by enabling the transition from direct LLM application usage to function generation, AskIt achieved significant speedups, as observed in our GSM8K benchmark experiments. Through these advancements, AskIt streamlines the integration of LLMs in software development, offering a more efficient, versatile approach for leveraging emergent abilities. The implementations of AskIt in TypeScript and Python are available at https://github.com/katsumiok/ts-askit and https://github.com/katsumiok/pyaskit, respectively.

Efficient state space models (SSMs), such as linear recurrent neural networks and linear attention variants, offer computational advantages over Transformers but struggle with tasks requiring long-range in-context retrieval-like text copying, associative recall, and question answering over long contexts. Previous efforts to address these challenges have focused on architectural modifications, often reintroducing computational inefficiencies. In this paper, we propose a novel training procedure, Birdie, that significantly enhances the in-context retrieval capabilities of SSMs without altering their architecture. Our approach combines bidirectional input processing with dynamic mixtures of specialized pre-training objectives, optimized via reinforcement learning. We introduce a new bidirectional SSM architecture that seamlessly transitions from bidirectional context processing to causal generation. Experimental evaluations demonstrate that Birdie markedly improves performance on retrieval-intensive tasks such as multi-number phone book lookup, long paragraph question-answering, and infilling. This narrows the performance gap with Transformers, while retaining computational efficiency. Our findings highlight the importance of training procedures in leveraging the fixed-state capacity of SSMs, offering a new direction to advance their capabilities. All code and pre-trained models are available at https://www.github.com/samblouir/birdie, with support for JAX and PyTorch.

The development of machine learning (ML) techniques has led to ample opportunities for developers to develop and deploy their own models. Hugging Face serves as an open source platform where developers can share and download other models in an effort to make ML development more collaborative. In order for models to be shared, they first need to be serialized. Certain Python serialization methods are considered unsafe, as they are vulnerable to object injection. This paper investigates the pervasiveness of these unsafe serialization methods across Hugging Face, and demonstrates through an exploitation approach, that models using unsafe serialization methods can be exploited and shared, creating an unsafe environment for ML developers. We investigate to what extent Hugging Face is able to flag repositories and files using unsafe serialization methods, and develop a technique to detect malicious models. Our results show that Hugging Face is home to a wide range of potentially vulnerable models.

REST APIs play important roles in enriching the action space of web agents, yet most API-based agents rely on curated and uniform toolsets that do not reflect the complexity of real-world APIs. Building tool-using agents for arbitrary domains remains a major challenge, as it requires reading unstructured API documentation, testing APIs and inferring correct parameters. We propose Doc2Agent, a scalable pipeline to build agents that can call Python-based tools generated from API documentation. Doc2Agent generates executable tools from API documentations and iteratively refines them using a code agent. We evaluate our approach on real-world APIs, WebArena APIs, and research APIs, producing validated tools. We achieved a 55\% relative performance improvement with 90\% lower cost compared to direct API calling on WebArena benchmark. A domain-specific agent built for glycomaterial science further demonstrates the pipeline's adaptability to complex, knowledge-rich tasks. Doc2Agent offers a generalizable solution for building tool agents from unstructured API documentation at scale.

Automated code generation is gaining significant importance in intelligent computer programming and system deployment. However, current approaches often face challenges in computational efficiency and lack robust mechanisms for code parsing and error correction. In this work, we propose a novel framework, PyCapsule, with a simple yet effective two-agent pipeline and efficient self-debugging modules for Python code generation. PyCapsule features sophisticated prompt inference, iterative error handling, and case testing, ensuring high generation stability, safety, and correctness. Empirically, PyCapsule achieves up to 5.7% improvement of success rate on HumanEval, 10.3% on HumanEval-ET, and 24.4% on BigCodeBench compared to the state-of-art methods. We also observe a decrease in normalized success rate given more self-debugging attempts, potentially affected by limited and noisy error feedback in retention. PyCapsule demonstrates broader impacts on advancing lightweight and efficient code generation for artificial intelligence systems.

Despite the huge success of Large Language Models (LLMs) in coding assistants like GitHub Copilot, these models struggle to understand the context present in the repository (e.g., imports, parent classes, files with similar names, etc.), thereby producing inaccurate code completions. This effect is more pronounced when using these assistants for repositories that the model has not seen during training, such as proprietary software or work-in-progress code projects. Recent work has shown the promise of using context from the repository during inference. In this work, we extend this idea and propose RepoFusion, a framework to train models to incorporate relevant repository context. Experiments on single-line code completion show that our models trained with repository context significantly outperform much larger code models as CodeGen-16B-multi (sim73times larger) and closely match the performance of the sim 70times larger StarCoderBase model that was trained with the Fill-in-the-Middle objective. We find these results to be a novel and compelling demonstration of the gains that training with repository context can bring. We carry out extensive ablation studies to investigate the impact of design choices such as context type, number of contexts, context length, and initialization within our framework. Lastly, we release Stack-Repo, a dataset of 200 Java repositories with permissive licenses and near-deduplicated files that are augmented with three types of repository contexts. Additionally, we are making available the code and trained checkpoints for our work. Our released resources can be found at https://huggingface.co/RepoFusion.

The advent of Large Language Models (LLMs) has spurred the development of coding agents for real-world code generation. As a widely used benchmark for evaluating the code generation capabilities of these agents, SWE-Bench uses real-world problems based on GitHub issues and their corresponding pull requests. However, the manually written test cases included in these pull requests are often insufficient, allowing generated patches to pass the tests without resolving the underlying issue. To address this challenge, we introduce UTGenerator, an LLM-driven test case generator that automatically analyzes codebases and dependencies to generate test cases for real-world Python projects. Building on UTGenerator, we propose UTBoost, a comprehensive framework for test case augmentation. In our evaluation, we identified 36 task instances with insufficient test cases and uncovered 345 erroneous patches incorrectly labeled as passed in the original SWE Bench. These corrections, impacting 40.9% of SWE-Bench Lite and 24.4% of SWE-Bench Verified leaderboard entries, yield 18 and 11 ranking changes, respectively.

Quantization has become a popular technique to compress neural networks and reduce compute cost, but most prior work focuses on studying quantization without changing the network size. Many real-world applications of neural networks have compute cost and memory budgets, which can be traded off with model quality by changing the number of parameters. In this work, we use ResNet as a case study to systematically investigate the effects of quantization on inference compute cost-quality tradeoff curves. Our results suggest that for each bfloat16 ResNet model, there are quantized models with lower cost and higher accuracy; in other words, the bfloat16 compute cost-quality tradeoff curve is Pareto-dominated by the 4-bit and 8-bit curves, with models primarily quantized to 4-bit yielding the best Pareto curve. Furthermore, we achieve state-of-the-art results on ImageNet for 4-bit ResNet-50 with quantization-aware training, obtaining a top-1 eval accuracy of 77.09%. We demonstrate the regularizing effect of quantization by measuring the generalization gap. The quantization method we used is optimized for practicality: It requires little tuning and is designed with hardware capabilities in mind. Our work motivates further research into optimal numeric formats for quantization, as well as the development of machine learning accelerators supporting these formats. As part of this work, we contribute a quantization library written in JAX, which is open-sourced at https://github.com/google-research/google-research/tree/master/aqt.

Interactive programming with interleaved code snippet cells and natural language markdown is recently gaining popularity in the form of Jupyter notebooks, which accelerate prototyping and collaboration. To study code generation conditioned on a long context history, we present JuICe, a corpus of 1.5 million examples with a curated test set of 3.7K instances based on online programming assignments. Compared with existing contextual code generation datasets, JuICe provides refined human-curated data, open-domain code, and an order of magnitude more training data. Using JuICe, we train models for two tasks: (1) generation of the API call sequence in a code cell, and (2) full code cell generation, both conditioned on the NL-Code history up to a particular code cell. Experiments using current baseline code generation models show that both context and distant supervision aid in generation, and that the dataset is challenging for current systems.

Large Language Models (LLMs) have demonstrated impressive capabilities in code generation. However, current evaluation datasets suffer from issues such as the lack of runnable test cases, deviation from the distribution of real-world code, and the ability to evaluate only the Python language. These limitations undermine the credibility of the evaluation results. To address these limitations, we introduce MRG-Bench (Multi-language Repository-level Code Generation Benchmark), a novel dataset that provides a more accurate evaluation of LLMs in practical repository-level code generation tasks. MRG-Bench has three main features: (1) practical data sourced from real-world code repositories that align to the practical distribution, (2) multiple programming languages support, including Python, Java, and Go, and (3) project-level runnable test cases to assess the quality of the generated code. Based on MRG-Bench, we conducted extensive experiments including large language models, long-context models, and RAG-related methods. These evaluation results demonstrate that current repository-level code generation techniques suffer from significant performance deficiencies. To further investigate why models fail, we designed novel experiments to annotate the underlying causes of generation errors. The results explicitly show that the majority of methods suffer from "difficulty in understanding user requirements," failing to comprehend their assigned tasks accurately. Moreover, the impact of different repository-level contexts on this issue exhibits significant disparities across different programming languages, suggesting that, in practice, specialized contextual information needs to be designed for different languages.

Software updates, including bug repair and feature additions, are frequent in modern applications but they often leave test suites outdated, resulting in undetected bugs and increased chances of system failures. A recent study by Meta revealed that 14%-22% of software failures stem from outdated tests that fail to reflect changes in the codebase. This highlights the need to keep tests in sync with code changes to ensure software reliability. In this paper, we present UTFix, a novel approach for repairing unit tests when their corresponding focal methods undergo changes. UTFix addresses two critical issues: assertion failure and reduced code coverage caused by changes in the focal method. Our approach leverages language models to repair unit tests by providing contextual information such as static code slices, dynamic code slices, and failure messages. We evaluate UTFix on our generated synthetic benchmarks (Tool-Bench), and real-world benchmarks. Tool- Bench includes diverse changes from popular open-source Python GitHub projects, where UTFix successfully repaired 89.2% of assertion failures and achieved 100% code coverage for 96 tests out of 369 tests. On the real-world benchmarks, UTFix repairs 60% of assertion failures while achieving 100% code coverage for 19 out of 30 unit tests. To the best of our knowledge, this is the first comprehensive study focused on unit test in evolving Python projects. Our contributions include the development of UTFix, the creation of Tool-Bench and real-world benchmarks, and the demonstration of the effectiveness of LLM-based methods in addressing unit test failures due to software evolution.

In this paper, we describe Function Assistant, a lightweight Python-based toolkit for querying and exploring source code repositories using natural language. The toolkit is designed to help end-users of a target API quickly find information about functions through high-level natural language queries and descriptions. For a given text query and background API, the tool finds candidate functions by performing a translation from the text to known representations in the API using the semantic parsing approach of Richardson and Kuhn (2017). Translations are automatically learned from example text-code pairs in example APIs. The toolkit includes features for building translation pipelines and query engines for arbitrary source code projects. To explore this last feature, we perform new experiments on 27 well-known Python projects hosted on Github.

Developers are sharing pre-trained Machine Learning (ML) models through a variety of model sharing platforms, such as Hugging Face, in an effort to make ML development more collaborative. To share the models, they must first be serialized. While there are many methods of serialization in Python, most of them are unsafe. To tame this insecurity, Hugging Face released safetensors as a way to mitigate the threats posed by unsafe serialization formats. In this context, this paper investigates developer's shifts towards using safetensors on Hugging Face in an effort to understand security practices in the ML development community, as well as how developers react to new methods of serialization. Our results find that more developers are adopting safetensors, and many safetensor adoptions were made by automated conversions of existing models by Hugging Face's conversion tool. We also found, however, that a majority of developers ignore the conversion tool's pull requests, and that while many developers are facing issues with using safetensors, they are eager to learn about and adapt the format.

Scikit-learn is an increasingly popular machine learning li- brary. Written in Python, it is designed to be simple and efficient, accessible to non-experts, and reusable in various contexts. In this paper, we present and discuss our design choices for the application programming interface (API) of the project. In particular, we describe the simple and elegant interface shared by all learning and processing units in the library and then discuss its advantages in terms of composition and reusability. The paper also comments on implementation details specific to the Python ecosystem and analyzes obstacles faced by users and developers of the library.

Code comments can help in program comprehension and are considered as important artifacts to help developers in software maintenance. However, the comments are mostly missing or are outdated, specially in complex software projects. As a result, several automatic comment generation models are developed as a solution. The recent models explore the integration of external knowledge resources such as Unified Modeling Language class diagrams to improve the generated comments. In this paper, we propose API2Com, a model that leverages the Application Programming Interface Documentations (API Docs) as a knowledge resource for comment generation. The API Docs include the description of the methods in more details and therefore, can provide better context in the generated comments. The API Docs are used along with the code snippets and Abstract Syntax Trees in our model. We apply the model on a large Java dataset of over 130,000 methods and evaluate it using both Transformer and RNN-base architectures. Interestingly, when API Docs are used, the performance increase is negligible. We therefore run different experiments to reason about the results. For methods that only contain one API, adding API Docs improves the results by 4% BLEU score on average (BLEU score is an automatic evaluation metric used in machine translation). However, as the number of APIs that are used in a method increases, the performance of the model in generating comments decreases due to long documentations used in the input. Our results confirm that the API Docs can be useful in generating better comments, but, new techniques are required to identify the most informative ones in a method rather than using all documentations simultaneously.

Automated unit test case generation tools facilitate test-driven development and support developers by suggesting tests intended to identify flaws in their code. Existing approaches are usually guided by the test coverage criteria, generating synthetic test cases that are often difficult for developers to read or understand. In this paper we propose AthenaTest, an approach that aims to generate unit test cases by learning from real-world focal methods and developer-written testcases. We formulate unit test case generation as a sequence-to-sequence learning task, adopting a two-step training procedure consisting of denoising pretraining on a large unsupervised Java corpus, and supervised finetuning for a downstream translation task of generating unit tests. We investigate the impact of natural language and source code pretraining, as well as the focal context information surrounding the focal method. Both techniques provide improvements in terms of validation loss, with pretraining yielding 25% relative improvement and focal context providing additional 11.1% improvement. We also introduce Methods2Test, the largest publicly available supervised parallel corpus of unit test case methods and corresponding focal methods in Java, which comprises 780K test cases mined from 91K open-source repositories from GitHub. We evaluate AthenaTest on five defects4j projects, generating 25K passing test cases covering 43.7% of the focal methods with only 30 attempts. We execute the test cases, collect test coverage information, and compare them with test cases generated by EvoSuite and GPT-3, finding that our approach outperforms GPT-3 and has comparable coverage w.r.t. EvoSuite. Finally, we survey professional developers on their preference in terms of readability, understandability, and testing effectiveness of the generated tests, showing overwhelmingly preference towards AthenaTest.

We present CRUXEval (Code Reasoning, Understanding, and eXecution Evaluation), a benchmark consisting of 800 Python functions (3-13 lines). Each function comes with an input-output pair, leading to two natural tasks: input prediction and output prediction. First, we propose a generic recipe for generating our execution benchmark which can be used to create future variation of the benchmark. Second, we evaluate twenty code models on our benchmark and discover that many recent high-scoring models on HumanEval do not show the same improvements on our benchmark. Third, we show that simple CoT and fine-tuning schemes can improve performance on our benchmark but remain far from solving it. The best setup, GPT-4 with chain of thought (CoT), achieves a pass@1 of 75% and 81% on input and output prediction, respectively. In contrast, Code Llama 34B achieves a pass@1 of 50% and 46% on input and output prediction, highlighting the gap between open and closed source models. As no model is close to acing CRUXEval, we provide examples of consistent GPT-4 failures on simple programs as a lens into its code reasoning capabilities and areas for improvement.

TypeScript and Python are two programming languages that support optional type annotations, which are useful but tedious to introduce and maintain. This has motivated automated type prediction: given an untyped program, produce a well-typed output program. Large language models (LLMs) are promising for type prediction, but there are challenges: fill-in-the-middle performs poorly, programs may not fit into the context window, generated types may not type check, and it is difficult to measure how well-typed the output program is. We address these challenges by building OpenTau, a search-based approach for type prediction that leverages large language models. We propose a new metric for type prediction quality, give a tree-based program decomposition that searches a space of generated types, and present fill-in-the-type fine-tuning for LLMs. We evaluate our work with a new dataset for TypeScript type prediction, and show that 47.4% of files type check (14.5% absolute improvement) with an overall rate of 3.3 type errors per file. All code, data, and models are available at: https://github.com/GammaTauAI/opentau.

Text Retrieval (TR) involves finding and retrieving text-based content relevant to a user's query from a large repository, with applications in real-world scenarios such as legal document retrieval. While most existing studies focus on English, limited work addresses Japanese contexts. In this paper, we introduce a new dataset specifically designed for Japanese legal contexts and propose a novel two-phase pipeline tailored to this domain. In the first phase, the model learns a broad understanding of global contexts, enhancing its generalization and adaptability to diverse queries. In the second phase, the model is fine-tuned to address complex queries specific to legal scenarios. Extensive experiments are conducted to demonstrate the superior performance of our method, which outperforms existing baselines. Furthermore, our pipeline proves effective in English contexts, surpassing comparable baselines on the MS MARCO dataset. We have made our code publicly available on GitHub, and the model checkpoints are accessible via HuggingFace.

Code completion models have made significant progress in recent years, yet current popular evaluation datasets, such as HumanEval and MBPP, predominantly focus on code completion tasks within a single file. This over-simplified setting falls short of representing the real-world software development scenario where repositories span multiple files with numerous cross-file dependencies, and accessing and understanding cross-file context is often required to complete the code correctly. To fill in this gap, we propose CrossCodeEval, a diverse and multilingual code completion benchmark that necessitates an in-depth cross-file contextual understanding to complete the code accurately. CrossCodeEval is built on a diverse set of real-world, open-sourced, permissively-licensed repositories in four popular programming languages: Python, Java, TypeScript, and C#. To create examples that strictly require cross-file context for accurate completion, we propose a straightforward yet efficient static-analysis-based approach to pinpoint the use of cross-file context within the current file. Extensive experiments on state-of-the-art code language models like CodeGen and StarCoder demonstrate that CrossCodeEval is extremely challenging when the relevant cross-file context is absent, and we see clear improvements when adding these context into the prompt. However, despite such improvements, the pinnacle of performance remains notably unattained even with the highest-performing model, indicating that CrossCodeEval is also capable of assessing model's capability in leveraging extensive context to make better code completion. Finally, we benchmarked various methods in retrieving cross-file context, and show that CrossCodeEval can also be used to measure the capability of code retrievers.

Automatically generating source code from natural language descriptions has been a growing field of research in recent years. However, current large-scale code generation models often encounter difficulties when selecting appropriate APIs for specific contexts. These models may generate APIs that do not meet requirements or refer to non-existent APIs in third-party libraries, especially for lesser-known or private libraries. Inspired by the process of human developers using tools to search APIs, we propose ToolCoder, a novel approach that integrates API search tools with existing models to assist in code generation and API selection. To teach our model to use tools, we introduce an automated data annotation method using ChatGPT to add tool usage information into the source code data and fine-tune code generation models. During inference, we integrate API search tools into the generation process so that our model can automatically use the search tool to get suggestions when selecting an API. Our experimental results demonstrate that ToolCoder exhibits excellent performance and generalization across five public and private library code generation benchmarks, with at least 6.21\% improvement on average pass@1 metrics and 9.64\% improvement on average pass@10 metrics compared to state-of-the-art methods. Furthermore, we show that our relatively small ToolCoder model is comparable to one of the current best models, GPT-3.5, highlighting the potential of incorporating programming tools into the code generation process.

Code completion has become an essential tool for daily software development. Existing evaluation benchmarks often employ static methods that do not fully capture the dynamic nature of real-world coding environments and face significant challenges, including limited context length, reliance on superficial evaluation metrics, and potential overfitting to training datasets. In this work, we introduce a novel framework for enhancing code completion in software development through the creation of a repository-level benchmark ExecRepoBench and the instruction corpora Repo-Instruct, aim at improving the functionality of open-source large language models (LLMs) in real-world coding scenarios that involve complex interdependencies across multiple files. ExecRepoBench includes 1.2K samples from active Python repositories. Plus, we present a multi-level grammar-based completion methodology conditioned on the abstract syntax tree to mask code fragments at various logical units (e.g. statements, expressions, and functions). Then, we fine-tune the open-source LLM with 7B parameters on Repo-Instruct to produce a strong code completion baseline model Qwen2.5-Coder-Instruct-C based on the open-source model. Qwen2.5-Coder-Instruct-C is rigorously evaluated against existing benchmarks, including MultiPL-E and ExecRepoBench, which consistently outperforms prior baselines across all programming languages. The deployment of can be used as a high-performance, local service for programming development\url{https://execrepobench.github.io/}.

For a complicated algorithm, its implementation by a human programmer usually starts with outlining a rough control flow followed by iterative enrichments, eventually yielding carefully generated syntactic structures and variables in a hierarchy. However, state-of-the-art large language models generate codes in a single pass, without intermediate warm-ups to reflect the structured thought process of "outline-then-detail". Inspired by the recent success of chain-of-thought prompting, we propose ChainCoder, a program synthesis language model that generates Python code progressively, i.e. from coarse to fine in multiple passes. We first decompose source code into layout frame components and accessory components via abstract syntax tree parsing to construct a hierarchical representation. We then reform our prediction target into a multi-pass objective, each pass generates a subsequence, which is concatenated in the hierarchy. Finally, a tailored transformer architecture is leveraged to jointly encode the natural language descriptions and syntactically aligned I/O data samples. Extensive evaluations show that ChainCoder outperforms state-of-the-arts, demonstrating that our progressive generation eases the reasoning procedure and guides the language model to generate higher-quality solutions. Our codes are available at: https://github.com/VITA-Group/ChainCoder.

In this work, we make the first attempt to evaluate LLMs in a more challenging code generation scenario, i.e. class-level code generation. We first manually construct the first class-level code generation benchmark ClassEval of 100 class-level Python code generation tasks with approximately 500 person-hours. Based on it, we then perform the first study of 11 state-of-the-art LLMs on class-level code generation. Based on our results, we have the following main findings. First, we find that all existing LLMs show much worse performance on class-level code generation compared to on standalone method-level code generation benchmarks like HumanEval; and the method-level coding ability cannot equivalently reflect the class-level coding ability among LLMs. Second, we find that GPT-4 and GPT-3.5 still exhibit dominate superior than other LLMs on class-level code generation, and the second-tier models includes Instruct-Starcoder, Instruct-Codegen, and Wizardcoder with very similar performance. Third, we find that generating the entire class all at once (i.e. holistic generation strategy) is the best generation strategy only for GPT-4 and GPT-3.5, while method-by-method generation (i.e. incremental and compositional) is better strategies for the other models with limited ability of understanding long instructions and utilizing the middle information. Lastly, we find the limited model ability of generating method-dependent code and discuss the frequent error types in generated classes. Our benchmark is available at https://github.com/FudanSELab/ClassEval.

Source code is rarely written in isolation. It depends significantly on the programmatic context, such as the class that the code would reside in. To study this phenomenon, we introduce the task of generating class member functions given English documentation and the programmatic context provided by the rest of the class. This task is challenging because the desired code can vary greatly depending on the functionality the class provides (e.g., a sort function may or may not be available when we are asked to "return the smallest element" in a particular member variable list). We introduce CONCODE, a new large dataset with over 100,000 examples consisting of Java classes from online code repositories, and develop a new encoder-decoder architecture that models the interaction between the method documentation and the class environment. We also present a detailed error analysis suggesting that there is significant room for future work on this task.

As researchers and practitioners apply Machine Learning to increasingly more software engineering problems, the approaches they use become more sophisticated. A lot of modern approaches utilize internal code structure in the form of an abstract syntax tree (AST) or its extensions: path-based representation, complex graph combining AST with additional edges. Even though the process of extracting ASTs from code can be done with different parsers, the impact of choosing a parser on the final model quality remains unstudied. Moreover, researchers often omit the exact details of extracting particular code representations. In this work, we evaluate two models, namely Code2Seq and TreeLSTM, in the method name prediction task backed by eight different parsers for the Java language. To unify the process of data preparation with different parsers, we develop SuperParser, a multi-language parser-agnostic library based on PathMiner. SuperParser facilitates the end-to-end creation of datasets suitable for training and evaluation of ML models that work with structural information from source code. Our results demonstrate that trees built by different parsers vary in their structure and content. We then analyze how this diversity affects the models' quality and show that the quality gap between the most and least suitable parsers for both models turns out to be significant. Finally, we discuss other features of the parsers that researchers and practitioners should take into account when selecting a parser along with the impact on the models' quality. The code of SuperParser is publicly available at https://doi.org/10.5281/zenodo.6366591. We also publish Java-norm, the dataset we use to evaluate the models: https://doi.org/10.5281/zenodo.6366599.

Statistical language modeling and translation with transformers have found many successful applications in program understanding and generation tasks, setting high benchmarks for tools in modern software development environments. The finite context window of these neural models means, however, that they will be unable to leverage the entire relevant context of large files and packages for any given task. While there are many efforts to extend the context window, we introduce an architecture-independent approach for leveraging the syntactic hierarchies of source code for incorporating entire file-level context into a fixed-length window. Using concrete syntax trees of each source file we extract syntactic hierarchies and integrate them into context window by selectively removing from view more specific, less relevant scopes for a given task. We evaluate this approach on code generation tasks and joint translation of natural language and source code in Python programming language, achieving a new state-of-the-art in code completion and summarization for Python in the CodeXGLUE benchmark. We also introduce new CodeXGLUE benchmarks for user-experience-motivated tasks: code completion with normalized literals, method body completion/code summarization conditioned on file-level context.

In this article we describe an efficient approach to guiding language model text generation with regular expressions and context-free grammars. Our approach adds little to no overhead to the token sequence generation process, and makes guided generation feasible in practice. An implementation is provided in the open source Python library Outlines.

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

Software testing is a critical aspect of software development, yet generating test cases remains a routine task for engineers. This paper presents a benchmark, CLOVER, to evaluate models' capabilities in generating and completing test cases under specific conditions. Spanning from simple assertion completions to writing test cases that cover specific code blocks across multiple files, these tasks are based on 12 python repositories, analyzing 845 problems with context lengths ranging from 4k to 128k tokens. Utilizing code testing frameworks, we propose a method to construct retrieval contexts using coverage information. While models exhibit comparable performance with short contexts, notable differences emerge with 16k contexts. Notably, models like GPT-4o and Claude 3.5 can effectively leverage relevant snippets; however, all models score below 35\% on the complex Task III, even with the oracle context provided, underscoring the benchmark's significance and the potential for model improvement. The benchmark is containerized for code execution across tasks, and we will release the code, data, and construction methodologies.

Code generation has emerged as a key task to automate software development by converting high-level descriptions into executable code. Large language models (LLMs) excel at this but depend heavily on input prompt quality.Manual prompt engineering can be time-consuming and inconsistent, limiting LLM effectiveness. This paper introduces Prochemy, an innovative method for automatically refining prompts to boost code generation. Prochemy overcomes manual prompt limitations by automating optimization, ensuring consistency during inference, and supporting multi-agent systems.It iteratively refines prompts based on model performance, using an optimized final prompt for improved consistency across tasks. We tested Prochemy on natural language-based code generation and translation tasks using three LLM series. Results indicate Prochemy enhances existing methods, improving performance by 5.0% for GPT-3.5-Turbo and 1.9% for GPT-4o over zero-shot baselines on HumanEval. In state-of-the-art LDB, Prochemy + LDB surpasses standalone methods by 1.2-1.8%. For code translation, Prochemy boosts GPT-4o's Java-to-Python (AVATAR) performance from 74.5 to 84.1 (+12.9%) and Python-to-Java from 66.8 to 78.2 (+17.1%). Moreover, Prochemy maintains strong performance when integrated with the o1-mini model, validating its efficacy in code tasks. Designed as plug-and-play, Prochemy optimizes prompts with minimal human input, bridging the gap between simple prompts and complex frameworks.

Multi-agent reinforcement learning (MARL) has emerged as a promising solution for learning complex and scalable coordination behaviors in multi-robot systems. However, established MARL platforms (e.g., SMAC and MPE) lack robotics relevance and hardware deployment, leaving multi-robot learning researchers to develop bespoke environments and hardware testbeds dedicated to the development and evaluation of their individual contributions. The Multi-Agent RL Benchmark and Learning Environment for the Robotarium (MARBLER) is an exciting recent step in providing a standardized robotics-relevant platform for MARL, by bridging the Robotarium testbed with existing MARL software infrastructure. However, MARBLER lacks support for parallelization and GPU/TPU execution, making the platform prohibitively slow compared to modern MARL environments and hindering adoption. We contribute JaxRobotarium, a Jax-powered end-to-end simulation, learning, deployment, and benchmarking platform for the Robotarium. JaxRobotarium enables rapid training and deployment of multi-robot RL (MRRL) policies with realistic robot dynamics and safety constraints, supporting parallelization and hardware acceleration. Our generalizable learning interface integrates easily with SOTA MARL libraries (e.g., JaxMARL). In addition, JaxRobotarium includes eight standardized coordination scenarios, including four novel scenarios that bring established MARL benchmark tasks (e.g., RWARE and Level-Based Foraging) to a robotics setting. We demonstrate that JaxRobotarium retains high simulation fidelity while achieving dramatic speedups over baseline (20x in training and 150x in simulation), and provides an open-access sim-to-real evaluation pipeline through the Robotarium testbed, accelerating and democratizing access to multi-robot learning research and evaluation. Our code is available at https://github.com/GT-STAR-Lab/JaxRobotarium.

Large language models that enhance software development tasks, such as code generation, code completion, and code question answering (QA), have been extensively studied in both academia and the industry. The models are integrated into popular intelligent IDEs like JetBrains and Cursor. Current benchmarks for evaluating models' code comprehension capabilities primarily focus on code generation or completion, often neglecting QA, which is a crucial aspect of understanding code. Existing code QA benchmarks are derived from code comments with predefined patterns (e.g., CodeQA) or focus on specific domains, such as education (e.g., CS1QA). These benchmarks fail to capture the real-world complexity of software engineering and user requirements for understanding code repositories. To address this gap, we introduce CoReQA, a benchmark for Code Repository-level question answering, constructed from GitHub issues and comments from 176 popular repositories across four programming languages. Since questions and answers may include both natural language and code snippets, traditional evaluation metrics such as BLEU are inadequate for assessing repository-level QA performance. Thus, we provide an LLM-as-a-judge framework to evaluate QA performance from five aspects. Based on CoReQA, we evaluate the performance of three baselines, including two short-context models using generic retrieval strategies and one long-context model that utilizes the entire repository context. Evaluation results show that state-of-the-art proprietary and long-context models struggle to address repository-level questions effectively. Our analysis highlights the limitations of language models in assisting developers in understanding repositories and suggests future directions for improving repository comprehension systems through effective context retrieval methodologies.

The LLM Agent, equipped with a code interpreter, is capable of automatically solving real-world coding tasks, such as data analysis and image editing. However, existing benchmarks primarily focus on either simplistic tasks, such as completing a few lines of code, or on extremely complex and specific tasks at the repository level, neither of which are representative of various daily coding tasks. To address this gap, we introduce PyBench, a benchmark encompassing five main categories of real-world tasks, covering more than 10 types of files. Given a high-level user query and related files, the LLM Agent needs to reason and execute Python code via a code interpreter for a few turns before making a formal response to fulfill the user's requirements. Successfully addressing tasks in PyBench demands a robust understanding of various Python packages, superior reasoning capabilities, and the ability to incorporate feedback from executed code. Our evaluations indicate that current open-source LLMs are struggling with these tasks. Hence, we conduct analysis and experiments on four kinds of datasets proving that comprehensive abilities are needed for PyBench. Our fine-tuned 8B size model: PyLlama3 achieves an exciting performance on PyBench which surpasses many 33B and 70B size models. Our Benchmark, Training Dataset, and Model are available at: https://github.com/Mercury7353/PyBench{https://github.com/Mercury7353/PyBench}

Language model (LM) agents, such as SWE-agent and OpenHands, have made progress toward automated issue resolution. However, existing approaches are often limited to Python-only issues and rely on pre-constructed containers in SWE-bench with reproduced issues, restricting their applicability to real-world and work for multi-language repositories. We present Prometheus, designed to resolve real-world issues beyond benchmark settings. Prometheus is a multi-agent system that transforms an entire code repository into a unified knowledge graph to guide context retrieval for issue resolution. Prometheus encodes files, abstract syntax trees, and natural language text into a graph of typed nodes and five general edge types to support multiple programming languages. Prometheus uses Neo4j for graph persistence, enabling scalable and structured reasoning over large codebases. Integrated by the DeepSeek-V3 model, Prometheus resolves 28.67% and 13.7% of issues on SWE-bench Lite and SWE-bench Multilingual, respectively, with an average API cost of 0.23 and 0.38 per issue. Prometheus resolves 10 unique issues not addressed by prior work and is the first to demonstrate effectiveness across seven programming languages. Moreover, it shows the ability to resolve real-world GitHub issues in the LangChain and OpenHands repositories. We have open-sourced Prometheus at: https://github.com/Pantheon-temple/Prometheus

In today's software world with its cornucopia of reusable software libraries, when a programmer is faced with a programming task that they suspect can be completed through the use of a library, they often look for code examples using a search engine and then manually adapt found examples to their specific context of use. We put forward a vision based on a new breed of developer tools that have the potential to largely automate this process. The key idea is to adapt code autocompletion tools such that they take into account not only the developer's already-written code but also the intent of the task the developer is trying to achieve next, formulated in plain natural language. We call this practice of enriching the code with natural language intent to facilitate its completion natural language-guided programming. To show that this idea is feasible we design, implement and benchmark a tool that solves this problem in the context of a specific domain (data science) and a specific programming language (Python). Central to the tool is the use of language models trained on a large corpus of documented code. Our initial experiments confirm the feasibility of the idea but also make it clear that we have only scratched the surface of what may become possible in the future. We end the paper with a comprehensive research agenda to stimulate additional research in the budding area of natural language-guided programming.

Code execution is a fundamental aspect of programming language semantics that reflects the exact behavior of the code. However, most pre-trained models for code intelligence ignore the execution trace and only rely on source code and syntactic structures. In this paper, we investigate how well pre-trained models can understand and perform code execution. We develop a mutation-based data augmentation technique to create a large-scale and realistic Python dataset and task for code execution, which challenges existing models such as Codex. We then present CodeExecutor, a Transformer model that leverages code execution pre-training and curriculum learning to enhance its semantic comprehension. We evaluate CodeExecutor on code execution and show its promising performance and limitations. We also demonstrate its potential benefits for code intelligence tasks such as zero-shot code-to-code search and text-to-code generation. Our analysis provides insights into the learning and generalization abilities of pre-trained models for code execution.

We introduce WebApp1K, a practical code-generation benchmark to measure LLM ability to develop web apps. This benchmark aims to calibrate LLM output and aid the models to progressively improve code correctness and functionality. The benchmark is lightweight and easy to run. We present the initial version of WebApp1K, and share our findings of running the benchmark against the latest frontier LLMs. First, open source LLMs deliver impressive performance, closely trailing behind GPT-4o and Claude 3.5. Second, model size has strong correlation with code correctness. Third, no prompting techniques have been found to lift performance either universally to all models, or significantly to a single model.

Density functional theory (DFT) stands as a cornerstone method in computational quantum chemistry and materials science due to its remarkable versatility and scalability. Yet, it suffers from limitations in accuracy, particularly when dealing with strongly correlated systems. To address these shortcomings, recent work has begun to explore how machine learning can expand the capabilities of DFT; an endeavor with many open questions and technical challenges. In this work, we present Grad DFT: a fully differentiable JAX-based DFT library, enabling quick prototyping and experimentation with machine learning-enhanced exchange-correlation energy functionals. Grad DFT employs a pioneering parametrization of exchange-correlation functionals constructed using a weighted sum of energy densities, where the weights are determined using neural networks. Moreover, Grad DFT encompasses a comprehensive suite of auxiliary functions, notably featuring a just-in-time compilable and fully differentiable self-consistent iterative procedure. To support training and benchmarking efforts, we additionally compile a curated dataset of experimental dissociation energies of dimers, half of which contain transition metal atoms characterized by strong electronic correlations. The software library is tested against experimental results to study the generalization capabilities of a neural functional across potential energy surfaces and atomic species, as well as the effect of training data noise on the resulting model accuracy.

Transformer-based language models for automatic code completion have shown great promise so far, yet the evaluation of these models rarely uses real data. This study provides both quantitative and qualitative assessments of three public code language models when completing real-world code. We first developed an open-source IDE extension, Code4Me, for the online evaluation of the models. We collected real auto-completion usage data for over a year from more than 1200 users, resulting in over 600K valid completions. These models were then evaluated using six standard metrics across twelve programming languages. Next, we conducted a qualitative study of 1690 real-world completion requests to identify the reasons behind the poor model performance. A comparative analysis of the models' performance in online and offline settings was also performed, using benchmark synthetic datasets and two masking strategies. Our findings suggest that while developers utilize code completion across various languages, the best results are achieved for mainstream languages such as Python and Java. InCoder outperformed the other models across all programming languages, highlighting the significance of training data and objectives. Our study also revealed that offline evaluations do not accurately reflect real-world scenarios. Upon qualitative analysis of the model's predictions, we found that 66.3% of failures were due to the models' limitations, 24.4% occurred due to inappropriate model usage in a development context, and 9.3% were valid requests that developers overwrote. Given these findings, we propose several strategies to overcome the current limitations. These include refining training objectives, improving resilience to typographical errors, adopting hybrid approaches, and enhancing implementations and usability.

Many applications need up-to-date copies of collections of changing Web resources. Such synchronization is currently achieved using ad-hoc or proprietary solutions. We propose ResourceSync, a general Web resource synchronization protocol that leverages XML Sitemaps. It provides a set of capabilities that can be combined in a modular manner to meet local or community requirements. We report on work to implement this protocol for arXiv.org and also provide an experimental prototype for the English Wikipedia as well as a client API.

Motivated by the growing demand for low-precision arithmetic in computational science, we exploit lower-precision emulation in Python -- widely regarded as the dominant programming language for numerical analysis and machine learning. Low-precision training has revolutionized deep learning by enabling more efficient computation and reduced memory and energy consumption while maintaining model fidelity. To better enable numerical experimentation with and exploration of low precision computation, we developed the Pychop library, which supports customizable floating-point formats and a comprehensive set of rounding modes in Python, allowing users to benefit from fast, low-precision emulation in numerous applications. Pychop also introduces interfaces for both PyTorch and JAX, enabling efficient low-precision emulation on GPUs for neural network training and inference with unparalleled flexibility. In this paper, we offer a comprehensive exposition of the design, implementation, validation, and practical application of Pychop, establishing it as a foundational tool for advancing efficient mixed-precision algorithms. Furthermore, we present empirical results on low-precision emulation for image classification and object detection using published datasets, illustrating the sensitivity of the use of low precision and offering valuable insights into its impact. Pychop enables in-depth investigations into the effects of numerical precision, facilitates the development of novel hardware accelerators, and integrates seamlessly into existing deep learning workflows. Software and experimental code are publicly available at https://github.com/inEXASCALE/pychop.

Despite the substantial success of Information Retrieval (IR) in various NLP tasks, most IR systems predominantly handle queries and corpora in natural language, neglecting the domain of code retrieval. Code retrieval is critically important yet remains under-explored, with existing methods and benchmarks inadequately representing the diversity of code in various domains and tasks. Addressing this gap, we present \name (Code Information Retrieval Benchmark), a robust and comprehensive benchmark specifically designed to assess code retrieval capabilities. \name comprises ten meticulously curated code datasets, spanning eight distinctive retrieval tasks across seven diverse domains. We first discuss the construction of \name and its diverse dataset composition. Further, we evaluate nine widely used retrieval models using \name, uncovering significant difficulties in performing code retrieval tasks even with state-of-the-art systems. To facilitate easy adoption and integration within existing research workflows, \name has been developed as a user-friendly Python framework, readily installable via pip. It shares same data schema as other popular benchmarks like MTEB and BEIR, enabling seamless cross-benchmark evaluations. Through \name, we aim to invigorate research in the code retrieval domain, providing a versatile benchmarking tool that encourages further development and exploration of code retrieval systems\url{ https://github.com/CoIR-team/coir}.

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.

Driven by the surge in code generation using large language models (LLMs), numerous benchmarks have emerged to evaluate these LLMs capabilities. We conducted a large-scale human evaluation of HumanEval and MBPP, two popular benchmarks for Python code generation, analyzing their diversity and difficulty. Our findings unveil a critical bias towards a limited set of programming concepts, neglecting most of the other concepts entirely. Furthermore, we uncover a worrying prevalence of easy tasks, potentially inflating model performance estimations. To address these limitations, we propose a novel benchmark, PythonSaga, featuring 185 hand-crafted prompts on a balanced representation of 38 programming concepts across diverse difficulty levels. The robustness of our benchmark is demonstrated by the poor performance of existing Code-LLMs.

With the rapid advancement of powerful large language models (LLMs) in recent years, a wide range of software engineering tasks can now be addressed using LLMs, significantly enhancing productivity and scalability. Numerous benchmark datasets have been developed to evaluate the coding capabilities of these models, while they primarily focus on problem-solving and issue-resolution tasks. In contrast, we introduce a new coding benchmark MIGRATION-BENCH with a distinct focus: code migration. MIGRATION-BENCH aims to serve as a comprehensive benchmark for migration from Java 8 to the latest long-term support (LTS) versions (Java 17, 21), MIGRATION-BENCH includes a full dataset and its subset selected with 5,102 and 300 repositories respectively. Selected is a representative subset curated for complexity and difficulty, offering a versatile resource to support research in the field of code migration. Additionally, we provide a comprehensive evaluation framework to facilitate rigorous and standardized assessment of LLMs on this challenging task. We further propose SD-Feedback and demonstrate that LLMs can effectively tackle repository-level code migration to Java 17. For the selected subset with Claude-3.5-Sonnet-v2, SD-Feedback achieves 62.33% and 27.00% success rate (pass@1) for minimal and maximal migration respectively. The benchmark dataset and source code are available at: https://huggingface.co/collections/AmazonScience and https://github.com/amazon-science/self_debug respectively.

With the success of large language models (LLMs) of code and their use as code assistants (e.g. Codex used in GitHub Copilot), techniques for introducing domain-specific knowledge in the prompt design process become important. In this work, we propose a framework called Repo-Level Prompt Generator that learns to generate example-specific prompts using prompt proposals. The prompt proposals take context from the entire repository, thereby incorporating both the structure of the repository and the context from other relevant files (e.g. imports, parent class files). Our technique doesn't require any access to the weights of the LLM, making it applicable in cases where we only have black-box access to the LLM. We conduct experiments on the task of single-line code-autocompletion using code repositories taken from Google Code archives. We demonstrate that an oracle constructed from our prompt proposals gives a remarkably high relative improvement of 36% over Codex, showing the quality of these proposals. Further, we show that when we train a model to predict a prompt proposal, we can achieve significant performance gains over Codex and other baselines. We release our code, data, and trained checkpoints at: https://github.com/shrivastavadisha/repo_level_prompt_generation.

Recent advances in retrieval-augmented generation (RAG) have initiated a new era in repository-level code completion. However, the invariable use of retrieval in existing methods exposes issues in both efficiency and robustness, with a large proportion of the retrieved contexts proving unhelpful or harmful to code language models (code LMs). In this paper, we propose a selective RAG framework to avoid retrieval when unnecessary. To power this framework, we design a self-supervised learning approach to enable a code LM to accurately self-evaluate whether retrieval can improve its output quality and robustly leverage the potentially noisy retrieved contexts. Using this LM as both the selective RAG policy and the generation model, our framework achieves state-of-the-art repository-level code completion performance on diverse benchmarks including RepoEval, CrossCodeEval, and CrossCodeLongEval, a new long-form code completion benchmark. Meanwhile, our analyses show that selectively retrieving brings as much as 70% inference speedup in the online serving setting without harming the performance. We further demonstrate that our framework is able to accommodate different generation models, retrievers, and programming languages. These advancements position our framework as an important step towards more accurate and efficient repository-level code completion.

This paper introduces DroneVis, a novel library designed to automate computer vision algorithms on Parrot drones. DroneVis offers a versatile set of features and provides a diverse range of computer vision tasks along with a variety of models to choose from. Implemented in Python, the library adheres to high-quality code standards, facilitating effortless customization and feature expansion according to user requirements. In addition, comprehensive documentation is provided, encompassing usage guidelines and illustrative use cases. Our documentation, code, and examples are available in https://github.com/ahmedheakl/drone-vis.

Test-driven development (TDD) is a widely-employed software development practice that mandates writing test cases based on requirements before writing the actual code. While writing test cases is the centerpiece of TDD, it is time-consuming, expensive, and often shunned by developers. To address these issues associated with TDD, automated test case generation approaches have recently been investigated. Such approaches take source code as input, but not the requirements. Therefore, existing work does not fully support true TDD, as actual code is required to generate test cases. In addition, current deep learning-based test case generation approaches are trained with one learning objective, i.e., to generate test cases that are exactly matched with the ground-truth test cases. However, such approaches may limit the model's ability to generate different yet correct test cases. In this paper, we introduce PyTester, a Text-to-Testcase generation approach that can automatically generate syntactically correct, executable, complete, and effective test cases while being aligned with a given natural language requirement. We evaluate PyTester on the public APPS benchmark dataset, and the results show that our Deep RL approach enables PyTester, a small language model, to outperform much larger language models like GPT3.5, StarCoder, and InCoder. Our findings suggest that future research could consider improving small over large LMs for better resource efficiency by integrating the SE domain knowledge into the design of reinforcement learning architecture.

Large Language Models (LLMs) are gaining popularity among software engineers. A crucial aspect of developing effective code generation LLMs is to evaluate these models using a robust benchmark. Evaluation benchmarks with quality issues can provide a false sense of performance. In this work, we conduct the first-of-its-kind study of the quality of prompts within benchmarks used to compare the performance of different code generation models. To conduct this study, we analyzed 3,566 prompts from 9 code generation benchmarks to identify quality issues in them. We also investigated whether fixing the identified quality issues in the benchmarks' prompts affects a model's performance. We also studied memorization issues of the evaluation dataset, which can put into question a benchmark's trustworthiness. We found that code generation evaluation benchmarks mainly focused on Python and coding exercises and had very limited contextual dependencies to challenge the model. These datasets and the developers' prompts suffer from quality issues like spelling and grammatical errors, unclear sentences to express developers' intent, and not using proper documentation style. Fixing all these issues in the benchmarks can lead to a better performance for Python code generation, but not a significant improvement was observed for Java code generation. We also found evidence that GPT-3.5-Turbo and CodeGen-2.5 models may have data contamination issues.

Code summarization is a critical task in natural language processing and software engineering, which aims to generate concise descriptions of source code. Recent advancements have improved the quality of these summaries, enhancing code readability and maintainability. However, the content of a repository or a class has not been considered in function code summarization. This study investigated the effectiveness of code summarization models beyond the function level, exploring the impact of class and repository contexts on the summary quality. The study involved revising benchmarks for evaluating models at class and repository levels, assessing baseline models, and evaluating LLMs with in-context learning to determine the enhancement of summary quality with additional context. The findings revealed that the fine-tuned state-of-the-art CodeT5+ base model excelled in code summarization, while incorporating few-shot learning and retrieved code chunks from RAG significantly enhanced the performance of LLMs in this task. Notably, the Deepseek Coder 1.3B and Starcoder2 15B models demonstrated substantial improvements in metrics such as BLEURT, METEOR, and BLEU-4 at both class and repository levels. Repository-level summarization exhibited promising potential but necessitates significant computational resources and gains from the inclusion of structured context. Lastly, we employed the recent SIDE code summarization metric in our evaluation. This study contributes to refining strategies for prompt engineering, few-shot learning, and RAG, addressing gaps in benchmarks for code summarization at various levels. Finally, we publish all study details, code, datasets, and results of evaluation in the GitHub repository available at https://github.com/kilimanj4r0/code-summarization-beyond-function-level.

Code completion, which aims to predict the following code token(s) according to the code context, can improve the productivity of software development. Recent work has proved that statistical language modeling with transformers can greatly improve the performance in the code completion task via learning from large-scale source code datasets. However, current approaches focus only on code context within the file or project, i.e. internal context. Our distinction is utilizing "external" context, inspired by human behaviors of copying from the related code snippets when writing code. Specifically, we propose a retrieval-augmented code completion framework, leveraging both lexical copying and referring to code with similar semantics by retrieval. We adopt a stage-wise training approach that combines a source code retriever and an auto-regressive language model for programming language. We evaluate our approach in the code completion task in Python and Java programming languages, achieving a state-of-the-art performance on CodeXGLUE benchmark.

Recent code large language models (LLMs) have shown promising performance in generating standalone functions but face limitations in repository-level code generation due to their lack of awareness of repository-level dependencies (e.g., user-defined attributes), resulting in dependency errors such as undefined-variable and no-member errors. In this work, we introduce ToolGen, an approach that integrates autocompletion tools into the code LLM generation process to address these dependencies. ToolGen comprises two main phases: Trigger Insertion and Model Fine-tuning (Offline), and Tool-integrated Code Generation (Online). During the offline phase, ToolGen augments functions within a given code corpus with a special mark token, indicating positions to trigger autocompletion tools. These augmented functions, along with their corresponding docstrings, are then used to fine-tune a selected code LLM. In the online phase, ToolGen iteratively generates functions by predicting tokens step-by-step using the fine-tuned LLM. Whenever a mark token is encountered, ToolGen invokes the autocompletion tool to suggest code completions and selects the most appropriate one. We conduct comprehensive experiments to evaluate ToolGen's effectiveness in repository-level code generation. To facilitate this evaluation, we create a benchmark comprising 680 real-world code repositories and introduce two new repository-level metrics: Dependency Coverage and Static Validity Rate. The results demonstrate that ToolGen significantly improves Dependency Coverage by 15.2% to 45.8% and Static Validity Rate by 10.9% to 42.2% across three distinct code LLMs, while maintaining competitive performance in widely-recognized similarity metrics. Furthermore, our generalizability evaluation confirms ToolGen's consistent performance when applied to diverse code LLMs, including various model architectures and scales.

Tool-augmented large language models (LLMs) have achieved remarkable progress in tackling a broad range of tasks. However, existing methods are mainly restricted to specifically designed tools and fail to fulfill complex instructions, having great limitations when confronted with real-world scenarios. In this paper, we explore a more realistic scenario by connecting LLMs with RESTful APIs, which adhere to the widely adopted REST software architectural style for web service development. To address the practical challenges of tackling complex instructions, we propose RestGPT, which exploits the power of LLMs and conducts a coarse-to-fine online planning mechanism to enhance the abilities of task decomposition and API selection. RestGPT also contains an API executor tailored for calling RESTful APIs, which can meticulously formulate parameters and parse API responses. To fully evaluate the performance of RestGPT, we propose RestBench, a high-quality benchmark which consists of two real-world scenarios and human-annotated instructions with gold solution paths. Experiments show that RestGPT is able to achieve impressive results in complex tasks and has strong robustness, which paves a new way towards AGI. RestGPT and RestBench is publicly available at https://restgpt.github.io/.

Large language models (LLMs) have shown remarkable ability in code generation with more than 90 pass@1 in solving Python coding problems in HumanEval and MBPP. Such high accuracy leads to the question: can LLMs replace human programmers? Existing manual crafted, simple, or single-line code generation benchmarks cannot answer this question due to their gap with real-world software development. To answer this question, we propose REPOCOD, a code generation benchmark with 980 problems collected from 11 popular real-world projects, with more than 58% of them requiring file-level or repository-level context information. In addition, REPOCOD has the longest average canonical solution length (331.6 tokens) and the highest average cyclomatic complexity (9.00) compared to existing benchmarks. In our evaluations on ten LLMs, none of the models can achieve more than 30 pass@1 on REPOCOD, disclosing the necessity of building stronger LLMs that can help developers in real-world software development.

This paper presents our system for SemEval-2025 Task 8: DataBench, Question-Answering over Tabular Data. The primary objective of this task is to perform question answering on given tabular datasets from diverse domains under two subtasks: DataBench QA (Subtask I) and DataBench Lite QA (Subtask II). To tackle both subtasks, we developed a zero-shot solution with a particular emphasis on leveraging Large Language Model (LLM)-based code generation. Specifically, we propose a Python code generation framework utilizing state-of-the-art open-source LLMs to generate executable Pandas code via optimized prompting strategies. Our experiments reveal that different LLMs exhibit varying levels of effectiveness in Python code generation. Additionally, results show that Python code generation achieves superior performance in tabular question answering compared to alternative approaches. Although our ranking among zero-shot systems is unknown at the time of this paper's submission, our system achieved eighth place in Subtask I and sixth place in Subtask~II among the 30 systems that outperformed the baseline in the open-source models category.

The BigCode community, an open-scientific collaboration working on the responsible development of Large Language Models for Code (Code LLMs), introduces StarCoder and StarCoderBase: 15.5B parameter models with 8K context length, infilling capabilities and fast large-batch inference enabled by multi-query attention. StarCoderBase is trained on 1 trillion tokens sourced from The Stack, a large collection of permissively licensed GitHub repositories with inspection tools and an opt-out process. We fine-tuned StarCoderBase on 35B Python tokens, resulting in the creation of StarCoder. We perform the most comprehensive evaluation of Code LLMs to date and show that StarCoderBase outperforms every open Code LLM that supports multiple programming languages and matches or outperforms the OpenAI code-cushman-001 model. Furthermore, StarCoder outperforms every model that is fine-tuned on Python, can be prompted to achieve 40\% pass@1 on HumanEval, and still retains its performance on other programming languages. We take several important steps towards a safe open-access model release, including an improved PII redaction pipeline and a novel attribution tracing tool, and make the StarCoder models publicly available under a more commercially viable version of the Open Responsible AI Model license.

Variance reduction (VR) techniques have contributed significantly to accelerating learning with massive datasets in the smooth and strongly convex setting (Schmidt et al., 2017; Johnson & Zhang, 2013; Roux et al., 2012). However, such techniques have not yet met the same success in the realm of large-scale deep learning due to various factors such as the use of data augmentation or regularization methods like dropout (Defazio & Bottou, 2019). This challenge has recently motivated the design of novel variance reduction techniques tailored explicitly for deep learning (Arnold et al., 2019; Ma & Yarats, 2018). This work is an additional step in this direction. In particular, we exploit the ubiquitous clustering structure of rich datasets used in deep learning to design a family of scalable variance reduced optimization procedures by combining existing optimizers (e.g., SGD+Momentum, Quasi Hyperbolic Momentum, Implicit Gradient Transport) with a multi-momentum strategy (Yuan et al., 2019). Our proposal leads to faster convergence than vanilla methods on standard benchmark datasets (e.g., CIFAR and ImageNet). It is robust to label noise and amenable to distributed optimization. We provide a parallel implementation in JAX.

Current search techniques are limited to standard RAG query-document applications. In this paper, we propose a novel technique to expand the code and index for predicting the required APIs, directly enabling high-quality, end-to-end code generation for auto-completion and agentic AI applications. We address the problem of API leaks in current code-to-code benchmark datasets by introducing a new dataset built from real-world ServiceNow Script Includes that capture the challenge of unclear API usage intent in the code. Our evaluation metrics show that this method achieves 87.86% top-40 retrieval accuracy, allowing the critical context with APIs needed for successful downstream code generation. To enable real-time predictions, we develop a comprehensive post-training pipeline that optimizes a compact 0.6B reranker through synthetic dataset generation, supervised fine-tuning, and reinforcement learning. This approach enables our compact reranker to outperform a much larger 8B model while maintaining 2.5x reduced latency, effectively addressing the nuances of enterprise-specific code without the computational overhead of larger models.