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Dec 9

DeepSeek-VL: Towards Real-World Vision-Language Understanding

We present DeepSeek-VL, an open-source Vision-Language (VL) Model designed for real-world vision and language understanding applications. Our approach is structured around three key dimensions: We strive to ensure our data is diverse, scalable, and extensively covers real-world scenarios including web screenshots, PDFs, OCR, charts, and knowledge-based content, aiming for a comprehensive representation of practical contexts. Further, we create a use case taxonomy from real user scenarios and construct an instruction tuning dataset accordingly. The fine-tuning with this dataset substantially improves the model's user experience in practical applications. Considering efficiency and the demands of most real-world scenarios, DeepSeek-VL incorporates a hybrid vision encoder that efficiently processes high-resolution images (1024 x 1024), while maintaining a relatively low computational overhead. This design choice ensures the model's ability to capture critical semantic and detailed information across various visual tasks. We posit that a proficient Vision-Language Model should, foremost, possess strong language abilities. To ensure the preservation of LLM capabilities during pretraining, we investigate an effective VL pretraining strategy by integrating LLM training from the beginning and carefully managing the competitive dynamics observed between vision and language modalities. The DeepSeek-VL family (both 1.3B and 7B models) showcases superior user experiences as a vision-language chatbot in real-world applications, achieving state-of-the-art or competitive performance across a wide range of visual-language benchmarks at the same model size while maintaining robust performance on language-centric benchmarks. We have made both 1.3B and 7B models publicly accessible to foster innovations based on this foundation model.

deepseek-ai DeepSeek
·
Mar 8, 2024 4

HEMM: Holistic Evaluation of Multimodal Foundation Models

Multimodal foundation models that can holistically process text alongside images, video, audio, and other sensory modalities are increasingly used in a variety of real-world applications. However, it is challenging to characterize and study progress in multimodal foundation models, given the range of possible modeling decisions, tasks, and domains. In this paper, we introduce Holistic Evaluation of Multimodal Models (HEMM) to systematically evaluate the capabilities of multimodal foundation models across a set of 3 dimensions: basic skills, information flow, and real-world use cases. Basic multimodal skills are internal abilities required to solve problems, such as learning interactions across modalities, fine-grained alignment, multi-step reasoning, and the ability to handle external knowledge. Information flow studies how multimodal content changes during a task through querying, translation, editing, and fusion. Use cases span domain-specific challenges introduced in real-world multimedia, affective computing, natural sciences, healthcare, and human-computer interaction applications. Through comprehensive experiments across the 30 tasks in HEMM, we (1) identify key dataset dimensions (e.g., basic skills, information flows, and use cases) that pose challenges to today's models, and (2) distill performance trends regarding how different modeling dimensions (e.g., scale, pre-training data, multimodal alignment, pre-training, and instruction tuning objectives) influence performance. Our conclusions regarding challenging multimodal interactions, use cases, and tasks requiring reasoning and external knowledge, the benefits of data and model scale, and the impacts of instruction tuning yield actionable insights for future work in multimodal foundation models.

  • 7 authors
·
Jul 3, 2024 1

Is It Really Long Context if All You Need Is Retrieval? Towards Genuinely Difficult Long Context NLP

Improvements in language models' capabilities have pushed their applications towards longer contexts, making long-context evaluation and development an active research area. However, many disparate use-cases are grouped together under the umbrella term of "long-context", defined simply by the total length of the model's input, including - for example - Needle-in-a-Haystack tasks, book summarization, and information aggregation. Given their varied difficulty, in this position paper we argue that conflating different tasks by their context length is unproductive. As a community, we require a more precise vocabulary to understand what makes long-context tasks similar or different. We propose to unpack the taxonomy of long-context based on the properties that make them more difficult with longer contexts. We propose two orthogonal axes of difficulty: (I) Diffusion: How hard is it to find the necessary information in the context? (II) Scope: How much necessary information is there to find? We survey the literature on long-context, provide justification for this taxonomy as an informative descriptor, and situate the literature with respect to it. We conclude that the most difficult and interesting settings, whose necessary information is very long and highly diffused within the input, is severely under-explored. By using a descriptive vocabulary and discussing the relevant properties of difficulty in long-context, we can implement more informed research in this area. We call for a careful design of tasks and benchmarks with distinctly long context, taking into account the characteristics that make it qualitatively different from shorter context.

  • 6 authors
·
Jun 29, 2024 1

Matching Table Metadata with Business Glossaries Using Large Language Models

Enterprises often own large collections of structured data in the form of large databases or an enterprise data lake. Such data collections come with limited metadata and strict access policies that could limit access to the data contents and, therefore, limit the application of classic retrieval and analysis solutions. As a result, there is a need for solutions that can effectively utilize the available metadata. In this paper, we study the problem of matching table metadata to a business glossary containing data labels and descriptions. The resulting matching enables the use of an available or curated business glossary for retrieval and analysis without or before requesting access to the data contents. One solution to this problem is to use manually-defined rules or similarity measures on column names and glossary descriptions (or their vector embeddings) to find the closest match. However, such approaches need to be tuned through manual labeling and cannot handle many business glossaries that contain a combination of simple as well as complex and long descriptions. In this work, we leverage the power of large language models (LLMs) to design generic matching methods that do not require manual tuning and can identify complex relations between column names and glossaries. We propose methods that utilize LLMs in two ways: a) by generating additional context for column names that can aid with matching b) by using LLMs to directly infer if there is a relation between column names and glossary descriptions. Our preliminary experimental results show the effectiveness of our proposed methods.

  • 6 authors
·
Sep 7, 2023 2

A Survey on Large Language Models for Code Generation

Large Language Models (LLMs) have garnered remarkable advancements across diverse code-related tasks, known as Code LLMs, particularly in code generation that generates source code with LLM from natural language descriptions. This burgeoning field has captured significant interest from both academic researchers and industry professionals due to its practical significance in software development, e.g., GitHub Copilot. Despite the active exploration of LLMs for a variety of code tasks, either from the perspective of natural language processing (NLP) or software engineering (SE) or both, there is a noticeable absence of a comprehensive and up-to-date literature review dedicated to LLM for code generation. In this survey, we aim to bridge this gap by providing a systematic literature review that serves as a valuable reference for researchers investigating the cutting-edge progress in LLMs for code generation. We introduce a taxonomy to categorize and discuss the recent developments in LLMs for code generation, covering aspects such as data curation, latest advances, performance evaluation, and real-world applications. In addition, we present a historical overview of the evolution of LLMs for code generation and offer an empirical comparison using the widely recognized HumanEval and MBPP benchmarks to highlight the progressive enhancements in LLM capabilities for code generation. We identify critical challenges and promising opportunities regarding the gap between academia and practical development. Furthermore, we have established a dedicated resource website (https://codellm.github.io) to continuously document and disseminate the most recent advances in the field.

  • 5 authors
·
Jun 1, 2024

AI Exchange Platforms

The rapid integration of Artificial Intelligence (AI) into organizational technology frameworks has transformed how organizations engage with AI-driven models, influencing both operational performance and strategic innovation. With the advent of foundation models, the importance of structured platforms for AI model exchange has become paramount for organizational efficacy and adaptability. However, a comprehensive framework to categorize and understand these platforms remains underexplored. To address this gap, our taxonomy provides a structured approach to categorize AI exchange platforms, examining key dimensions and characteristics, as well as revealing interesting interaction patterns between public research institutions and organizations: Some platforms leverage peer review as a mechanism for quality control, and provide mechanisms for online testing, deploying, and customization of models. Our paper is beneficial to practitioners seeking to understand challenges and opportunities that arise from AI exchange platforms. For academics, the taxonomy serves as a foundation for further research into the evolution, impact, and best practices associated with AI model sharing and utilization in different contexts. Additionally, our study provides insights into the evolving role of AI in various industries, highlighting the importance of adaptability and innovation in platform design. This paper serves as a critical resource for understanding the dynamic interplay between technology, business models, and user engagement in the rapidly growing domain of AI model exchanges pointing also towards possible future evolution.

  • 2 authors
·
Oct 7

AI4Research: A Survey of Artificial Intelligence for Scientific Research

Recent advancements in artificial intelligence (AI), particularly in large language models (LLMs) such as OpenAI-o1 and DeepSeek-R1, have demonstrated remarkable capabilities in complex domains such as logical reasoning and experimental coding. Motivated by these advancements, numerous studies have explored the application of AI in the innovation process, particularly in the context of scientific research. These AI technologies primarily aim to develop systems that can autonomously conduct research processes across a wide range of scientific disciplines. Despite these significant strides, a comprehensive survey on AI for Research (AI4Research) remains absent, which hampers our understanding and impedes further development in this field. To address this gap, we present a comprehensive survey and offer a unified perspective on AI4Research. Specifically, the main contributions of our work are as follows: (1) Systematic taxonomy: We first introduce a systematic taxonomy to classify five mainstream tasks in AI4Research. (2) New frontiers: Then, we identify key research gaps and highlight promising future directions, focusing on the rigor and scalability of automated experiments, as well as the societal impact. (3) Abundant applications and resources: Finally, we compile a wealth of resources, including relevant multidisciplinary applications, data corpora, and tools. We hope our work will provide the research community with quick access to these resources and stimulate innovative breakthroughs in AI4Research.

  • 16 authors
·
Jul 2

Code Red! On the Harmfulness of Applying Off-the-shelf Large Language Models to Programming Tasks

Nowadays, developers increasingly rely on solutions powered by Large Language Models (LLM) to assist them with their coding tasks. This makes it crucial to align these tools with human values to prevent malicious misuse. In this paper, we propose a comprehensive framework for assessing the potential harmfulness of LLMs within the software engineering domain. We begin by developing a taxonomy of potentially harmful software engineering scenarios and subsequently, create a dataset of prompts based on this taxonomy. To systematically assess the responses, we design and validate an automatic evaluator that classifies the outputs of a variety of LLMs both open-source and closed-source models, as well as general-purpose and code-specific LLMs. Furthermore, we investigate the impact of models size, architecture family, and alignment strategies on their tendency to generate harmful content. The results show significant disparities in the alignment of various LLMs for harmlessness. We find that some models and model families, such as Openhermes, are more harmful than others and that code-specific models do not perform better than their general-purpose counterparts. Notably, some fine-tuned models perform significantly worse than their base-models due to their design choices. On the other side, we find that larger models tend to be more helpful and are less likely to respond with harmful information. These results highlight the importance of targeted alignment strategies tailored to the unique challenges of software engineering tasks and provide a foundation for future work in this critical area.

  • 5 authors
·
Apr 2

The Responsible Foundation Model Development Cheatsheet: A Review of Tools & Resources

Foundation model development attracts a rapidly expanding body of contributors, scientists, and applications. To help shape responsible development practices, we introduce the Foundation Model Development Cheatsheet: a growing collection of 250+ tools and resources spanning text, vision, and speech modalities. We draw on a large body of prior work to survey resources (e.g. software, documentation, frameworks, guides, and practical tools) that support informed data selection, processing, and understanding, precise and limitation-aware artifact documentation, efficient model training, advance awareness of the environmental impact from training, careful model evaluation of capabilities, risks, and claims, as well as responsible model release, licensing and deployment practices. We hope this curated collection of resources helps guide more responsible development. The process of curating this list, enabled us to review the AI development ecosystem, revealing what tools are critically missing, misused, or over-used in existing practices. We find that (i) tools for data sourcing, model evaluation, and monitoring are critically under-serving ethical and real-world needs, (ii) evaluations for model safety, capabilities, and environmental impact all lack reproducibility and transparency, (iii) text and particularly English-centric analyses continue to dominate over multilingual and multi-modal analyses, and (iv) evaluation of systems, rather than just models, is needed so that capabilities and impact are assessed in context.

  • 23 authors
·
Jun 24, 2024

Diagnosing Failure Root Causes in Platform-Orchestrated Agentic Systems: Dataset, Taxonomy, and Benchmark

Agentic systems consisting of multiple LLM-driven agents coordinating through tools and structured interactions, are increasingly deployed for complex reasoning and problem-solving tasks. At the same time, emerging low-code and template-based agent development platforms (e.g., Dify) enable users to rapidly build and orchestrate agentic systems, which we refer to as platform-orchestrated agentic systems. However, these systems are also fragile and it remains unclear how to systematically identify their potential failure root cause. This paper presents a study of root cause identification of these platform-orchestrated agentic systems. To support this initiative, we construct a dataset AgentFail containing 307 failure logs from ten agentic systems, each with fine-grained annotations linking failures to their root causes. We additionally utilize counterfactual reasoning-based repair strategy to ensure the reliability of the annotation. Building on the dataset, we develop a taxonomy that characterizes failure root causes and analyze their distribution across different platforms and task domains. Furthermore, we introduce a benchmark that leverages LLMs for automatically identifying root causes, in which we also utilize the proposed taxonomy as guidance for LLMs. Results show that the taxonomy can largely improve the performance, thereby confirming its utility. Nevertheless, the accuracy of root cause identification reaches at most 33.6%, which indicates that this task still remains challenging. In light of these results, we also provide actionable guidelines for building such agentic systems. In summary, this paper provides a reliable dataset of failure root cause for platform-orchestrated agentic systems, corresponding taxonomy and benchmark, which serves as a foundation for advancing the development of more reliable agentic systems.

  • 7 authors
·
Sep 28

Doing More with Less -- Implementing Routing Strategies in Large Language Model-Based Systems: An Extended Survey

Large Language Models (LLM)-based systems, i.e. interconnected elements that include an LLM as a central component (e.g., conversational agents), are typically monolithic static architectures that rely on a single LLM for all user queries. However, they often require different preprocessing strategies, levels of reasoning, or knowledge. Generalist LLMs (i.e. GPT-4), trained on very large multi-topic corpora, can perform well in a variety of tasks. However, they require significant financial, energy, and hardware resources that may not be justified for basic tasks. This implies potentially investing in unnecessary costs for a given query. To overcome this problem, a routing mechanism routes user queries to the most suitable components, such as smaller LLMs or experts in specific topics. This approach may improve response quality while minimising costs. Routing can be expanded to other components of the conversational agent architecture, such as the selection of optimal embedding strategies. This paper explores key considerations for integrating routing into LLM-based systems, focusing on resource management, cost definition, and strategy selection. Our main contributions include a formalisation of the problem, a novel taxonomy of existing approaches emphasising relevance and resource efficiency, and a comparative analysis of these strategies in relation to industry practices. Finally, we identify critical challenges and directions for future research.

  • 6 authors
·
Feb 1

Domain Specialization as the Key to Make Large Language Models Disruptive: A Comprehensive Survey

Large language models (LLMs) have significantly advanced the field of natural language processing (NLP), providing a highly useful, task-agnostic foundation for a wide range of applications. However, directly applying LLMs to solve sophisticated problems in specific domains meets many hurdles, caused by the heterogeneity of domain data, the sophistication of domain knowledge, the uniqueness of domain objectives, and the diversity of the constraints (e.g., various social norms, cultural conformity, religious beliefs, and ethical standards in the domain applications). Domain specification techniques are key to make large language models disruptive in many applications. Specifically, to solve these hurdles, there has been a notable increase in research and practices conducted in recent years on the domain specialization of LLMs. This emerging field of study, with its substantial potential for impact, necessitates a comprehensive and systematic review to better summarize and guide ongoing work in this area. In this article, we present a comprehensive survey on domain specification techniques for large language models, an emerging direction critical for large language model applications. First, we propose a systematic taxonomy that categorizes the LLM domain-specialization techniques based on the accessibility to LLMs and summarizes the framework for all the subcategories as well as their relations and differences to each other. Second, we present an extensive taxonomy of critical application domains that can benefit dramatically from specialized LLMs, discussing their practical significance and open challenges. Last, we offer our insights into the current research status and future trends in this area.

  • 24 authors
·
May 29, 2023

Deep Learning Model Reuse in the HuggingFace Community: Challenges, Benefit and Trends

The ubiquity of large-scale Pre-Trained Models (PTMs) is on the rise, sparking interest in model hubs, and dedicated platforms for hosting PTMs. Despite this trend, a comprehensive exploration of the challenges that users encounter and how the community leverages PTMs remains lacking. To address this gap, we conducted an extensive mixed-methods empirical study by focusing on discussion forums and the model hub of HuggingFace, the largest public model hub. Based on our qualitative analysis, we present a taxonomy of the challenges and benefits associated with PTM reuse within this community. We then conduct a quantitative study to track model-type trends and model documentation evolution over time. Our findings highlight prevalent challenges such as limited guidance for beginner users, struggles with model output comprehensibility in training or inference, and a lack of model understanding. We also identified interesting trends among models where some models maintain high upload rates despite a decline in topics related to them. Additionally, we found that despite the introduction of model documentation tools, its quantity has not increased over time, leading to difficulties in model comprehension and selection among users. Our study sheds light on new challenges in reusing PTMs that were not reported before and we provide recommendations for various stakeholders involved in PTM reuse.

  • 5 authors
·
Jan 23, 2024 1

Enhancing Large Language Models for Text-to-Testcase Generation

Context: Test-driven development (TDD) is a widely employed software development practice that involves developing test cases based on requirements prior to writing the code. Although various methods for automated test case generation have been proposed, they are not specifically tailored for TDD, where requirements instead of code serve as input. Objective: In this paper, we introduce a text-to-testcase generation approach based on a large language model (GPT-3.5) that is fine-tuned on our curated dataset with an effective prompt design. Method: Our approach involves enhancing the capabilities of basic GPT-3.5 for text-to-testcase generation task that is fine-tuned on our curated dataset with an effective prompting design. We evaluated the effectiveness of our approach using a span of five large-scale open-source software projects. Results: Our approach generated 7k test cases for open source projects, achieving 78.5% syntactic correctness, 67.09% requirement alignment, and 61.7% code coverage, which substantially outperforms all other LLMs (basic GPT-3.5, Bloom, and CodeT5). In addition, our ablation study demonstrates the substantial performance improvement of the fine-tuning and prompting components of the GPT-3.5 model. Conclusions: These findings lead us to conclude that fine-tuning and prompting should be considered in the future when building a language model for the text-to-testcase generation task

  • 4 authors
·
Feb 19, 2024

Novice Developers' Perspectives on Adopting LLMs for Software Development: A Systematic Literature Review

Following the rise of large language models (LLMs), many studies have emerged in recent years focusing on exploring the adoption of LLM-based tools for software development by novice developers: computer science/software engineering students and early-career industry developers with two years or less of professional experience. These studies have sought to understand the perspectives of novice developers on using these tools, a critical aspect of the successful adoption of LLMs in software engineering. To systematically collect and summarise these studies, we conducted a systematic literature review (SLR) following the guidelines by Kitchenham et al. on 80 primary studies published between April 2022 and June 2025 to answer four research questions (RQs). In answering RQ1, we categorised the study motivations and methodological approaches. In RQ2, we identified the software development tasks for which novice developers use LLMs. In RQ3, we categorised the advantages, challenges, and recommendations discussed in the studies. Finally, we discuss the study limitations and future research needs suggested in the primary studies in answering RQ4. Throughout the paper, we also indicate directions for future work and implications for software engineering researchers, educators, and developers. Our research artifacts are publicly available at https://github.com/Samuellucas97/SupplementaryInfoPackage-SLR.

  • 4 authors
·
Mar 10

Toward General-Purpose Robots via Foundation Models: A Survey and Meta-Analysis

Building general-purpose robots that can operate seamlessly, in any environment, with any object, and utilizing various skills to complete diverse tasks has been a long-standing goal in Artificial Intelligence. Unfortunately, however, most existing robotic systems have been constrained - having been designed for specific tasks, trained on specific datasets, and deployed within specific environments. These systems usually require extensively-labeled data, rely on task-specific models, have numerous generalization issues when deployed in real-world scenarios, and struggle to remain robust to distribution shifts. Motivated by the impressive open-set performance and content generation capabilities of web-scale, large-capacity pre-trained models (i.e., foundation models) in research fields such as Natural Language Processing (NLP) and Computer Vision (CV), we devote this survey to exploring (i) how these existing foundation models from NLP and CV can be applied to the field of robotics, and also exploring (ii) what a robotics-specific foundation model would look like. We begin by providing an overview of what constitutes a conventional robotic system and the fundamental barriers to making it universally applicable. Next, we establish a taxonomy to discuss current work exploring ways to leverage existing foundation models for robotics and develop ones catered to robotics. Finally, we discuss key challenges and promising future directions in using foundation models for enabling general-purpose robotic systems. We encourage readers to view our ``living`` GitHub repository of resources, including papers reviewed in this survey as well as related projects and repositories for developing foundation models for robotics.

  • 20 authors
·
Dec 14, 2023

MeSH Term Suggestion for Systematic Review Literature Search

High-quality medical systematic reviews require comprehensive literature searches to ensure the recommendations and outcomes are sufficiently reliable. Indeed, searching for relevant medical literature is a key phase in constructing systematic reviews and often involves domain (medical researchers) and search (information specialists) experts in developing the search queries. Queries in this context are highly complex, based on Boolean logic, include free-text terms and index terms from standardised terminologies (e.g., MeSH), and are difficult and time-consuming to build. The use of MeSH terms, in particular, has been shown to improve the quality of the search results. However, identifying the correct MeSH terms to include in a query is difficult: information experts are often unfamiliar with the MeSH database and unsure about the appropriateness of MeSH terms for a query. Naturally, the full value of the MeSH terminology is often not fully exploited. This paper investigates methods to suggest MeSH terms based on an initial Boolean query that includes only free-text terms. These methods promise to automatically identify highly effective MeSH terms for inclusion in a systematic review query. Our study contributes an empirical evaluation of several MeSH term suggestion methods. We perform an extensive analysis of the retrieval, ranking, and refinement of MeSH term suggestions for each method and how these suggestions impact the effectiveness of Boolean queries.

  • 5 authors
·
Dec 1, 2021

Experimenting with Multi-Agent Software Development: Towards a Unified Platform

Large language models are redefining software engineering by implementing AI-powered techniques throughout the whole software development process, including requirement gathering, software architecture, code generation, testing, and deployment. However, it is still difficult to develop a cohesive platform that consistently produces the best outcomes across all stages. The objective of this study is to develop a unified platform that utilizes multiple artificial intelligence agents to automate the process of transforming user requirements into well-organized deliverables. These deliverables include user stories, prioritization, and UML sequence diagrams, along with the modular approach to APIs, unit tests, and end-to-end tests. Additionally, the platform will organize tasks, perform security and compliance, and suggest design patterns and improvements for non-functional requirements. We allow users to control and manage each phase according to their preferences. In addition, the platform provides security and compliance checks following European standards and proposes design optimizations. We use multiple models, such as GPT-3.5, GPT-4, and Llama3 to enable to generation of modular code as per user choice. The research also highlights the limitations and future research discussions to overall improve the software development life cycle. The source code for our uniform platform is hosted on GitHub, enabling additional experimentation and supporting both research and practical uses. \end

  • 6 authors
·
Jun 8, 2024

On building machine learning pipelines for Android malware detection: a procedural survey of practices, challenges and opportunities

As the smartphone market leader, Android has been a prominent target for malware attacks. The number of malicious applications (apps) identified for it has increased continually over the past decade, creating an immense challenge for all parties involved. For market holders and researchers, in particular, the large number of samples has made manual malware detection unfeasible, leading to an influx of research that investigate Machine Learning (ML) approaches to automate this process. However, while some of the proposed approaches achieve high performance, rapidly evolving Android malware has made them unable to maintain their accuracy over time. This has created a need in the community to conduct further research, and build more flexible ML pipelines. Doing so, however, is currently hindered by a lack of systematic overview of the existing literature, to learn from and improve upon the existing solutions. Existing survey papers often focus only on parts of the ML process (e.g., data collection or model deployment), while omitting other important stages, such as model evaluation and explanation. In this paper, we address this problem with a review of 42 highly-cited papers, spanning a decade of research (from 2011 to 2021). We introduce a novel procedural taxonomy of the published literature, covering how they have used ML algorithms, what features they have engineered, which dimensionality reduction techniques they have employed, what datasets they have employed for training, and what their evaluation and explanation strategies are. Drawing from this taxonomy, we also identify gaps in knowledge and provide ideas for improvement and future work.

  • 6 authors
·
Jun 12, 2023

A Comprehensive Survey of Deep Research: Systems, Methodologies, and Applications

This survey examines the rapidly evolving field of Deep Research systems -- AI-powered applications that automate complex research workflows through the integration of large language models, advanced information retrieval, and autonomous reasoning capabilities. We analyze more than 80 commercial and non-commercial implementations that have emerged since 2023, including OpenAI/Deep Research, Gemini/Deep Research, Perplexity/Deep Research, and numerous open-source alternatives. Through comprehensive examination, we propose a novel hierarchical taxonomy that categorizes systems according to four fundamental technical dimensions: foundation models and reasoning engines, tool utilization and environmental interaction, task planning and execution control, and knowledge synthesis and output generation. We explore the architectural patterns, implementation approaches, and domain-specific adaptations that characterize these systems across academic, scientific, business, and educational applications. Our analysis reveals both the significant capabilities of current implementations and the technical and ethical challenges they present regarding information accuracy, privacy, intellectual property, and accessibility. The survey concludes by identifying promising research directions in advanced reasoning architectures, multimodal integration, domain specialization, human-AI collaboration, and ecosystem standardization that will likely shape the future evolution of this transformative technology. By providing a comprehensive framework for understanding Deep Research systems, this survey contributes to both the theoretical understanding of AI-augmented knowledge work and the practical development of more capable, responsible, and accessible research technologies. The paper resources can be viewed at https://github.com/scienceaix/deepresearch.

  • 2 authors
·
Jun 14

FAIR Jupyter: a knowledge graph approach to semantic sharing and granular exploration of a computational notebook reproducibility dataset

The way in which data are shared can affect their utility and reusability. Here, we demonstrate how data that we had previously shared in bulk can be mobilized further through a knowledge graph that allows for much more granular exploration and interrogation. The original dataset is about the computational reproducibility of GitHub-hosted Jupyter notebooks associated with biomedical publications. It contains rich metadata about the publications, associated GitHub repositories and Jupyter notebooks, and the notebooks' reproducibility. We took this dataset, converted it into semantic triples and loaded these into a triple store to create a knowledge graph, FAIR Jupyter, that we made accessible via a web service. This enables granular data exploration and analysis through queries that can be tailored to specific use cases. Such queries may provide details about any of the variables from the original dataset, highlight relationships between them or combine some of the graph's content with materials from corresponding external resources. We provide a collection of example queries addressing a range of use cases in research and education. We also outline how sets of such queries can be used to profile specific content types, either individually or by class. We conclude by discussing how such a semantically enhanced sharing of complex datasets can both enhance their FAIRness, i.e., their findability, accessibility, interoperability, and reusability, and help identify and communicate best practices, particularly with regards to data quality, standardization, automation and reproducibility.

  • 2 authors
·
Apr 19, 2024

TaxoAdapt: Aligning LLM-Based Multidimensional Taxonomy Construction to Evolving Research Corpora

The rapid evolution of scientific fields introduces challenges in organizing and retrieving scientific literature. While expert-curated taxonomies have traditionally addressed this need, the process is time-consuming and expensive. Furthermore, recent automatic taxonomy construction methods either (1) over-rely on a specific corpus, sacrificing generalizability, or (2) depend heavily on the general knowledge of large language models (LLMs) contained within their pre-training datasets, often overlooking the dynamic nature of evolving scientific domains. Additionally, these approaches fail to account for the multi-faceted nature of scientific literature, where a single research paper may contribute to multiple dimensions (e.g., methodology, new tasks, evaluation metrics, benchmarks). To address these gaps, we propose TaxoAdapt, a framework that dynamically adapts an LLM-generated taxonomy to a given corpus across multiple dimensions. TaxoAdapt performs iterative hierarchical classification, expanding both the taxonomy width and depth based on corpus' topical distribution. We demonstrate its state-of-the-art performance across a diverse set of computer science conferences over the years to showcase its ability to structure and capture the evolution of scientific fields. As a multidimensional method, TaxoAdapt generates taxonomies that are 26.51% more granularity-preserving and 50.41% more coherent than the most competitive baselines judged by LLMs.

  • 6 authors
·
Jun 12 2

AI Agentic Programming: A Survey of Techniques, Challenges, and Opportunities

AI agentic programming is an emerging paradigm in which large language models (LLMs) autonomously plan, execute, and interact with external tools like compilers, debuggers, and version control systems to iteratively perform complex software development tasks. Unlike conventional code generation tools, agentic systems are capable of decomposing high-level goals, coordinating multi-step processes, and adapting their behavior based on intermediate feedback. These capabilities are transforming the software development practice. As this emerging field evolves rapidly, there is a need to define its scope, consolidate its technical foundations, and identify open research challenges. This survey provides a comprehensive and timely review of AI agentic programming. We introduce a taxonomy of agent behaviors and system architectures, and examine core techniques including planning, memory and context management, tool integration, and execution monitoring. We also analyze existing benchmarks and evaluation methodologies used to assess coding agent performance. Our study identifies several key challenges, including limitations in handling long context, a lack of persistent memory across tasks, and concerns around safety, alignment with user intent, and collaboration with human developers. We discuss emerging opportunities to improve the reliability, adaptability, and transparency of agentic systems. By synthesizing recent advances and outlining future directions, this survey aims to provide a foundation for research and development in building the next generation of intelligent and trustworthy AI coding agents.

  • 4 authors
·
Aug 14

Data Cards: Purposeful and Transparent Dataset Documentation for Responsible AI

As research and industry moves towards large-scale models capable of numerous downstream tasks, the complexity of understanding multi-modal datasets that give nuance to models rapidly increases. A clear and thorough understanding of a dataset's origins, development, intent, ethical considerations and evolution becomes a necessary step for the responsible and informed deployment of models, especially those in people-facing contexts and high-risk domains. However, the burden of this understanding often falls on the intelligibility, conciseness, and comprehensiveness of the documentation. It requires consistency and comparability across the documentation of all datasets involved, and as such documentation must be treated as a user-centric product in and of itself. In this paper, we propose Data Cards for fostering transparent, purposeful and human-centered documentation of datasets within the practical contexts of industry and research. Data Cards are structured summaries of essential facts about various aspects of ML datasets needed by stakeholders across a dataset's lifecycle for responsible AI development. These summaries provide explanations of processes and rationales that shape the data and consequently the models, such as upstream sources, data collection and annotation methods; training and evaluation methods, intended use; or decisions affecting model performance. We also present frameworks that ground Data Cards in real-world utility and human-centricity. Using two case studies, we report on desirable characteristics that support adoption across domains, organizational structures, and audience groups. Finally, we present lessons learned from deploying over 20 Data Cards.

  • 3 authors
·
Apr 3, 2022

CoIR: A Comprehensive Benchmark for Code Information Retrieval Models

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}.

  • 9 authors
·
Jul 3, 2024

Efficient and Green Large Language Models for Software Engineering: Vision and the Road Ahead

Large Language Models (LLMs) have recently shown remarkable capabilities in various software engineering tasks, spurring the rapid growth of the Large Language Models for Software Engineering (LLM4SE) area. However, limited attention has been paid to developing efficient LLM4SE techniques that demand minimal computational cost, time, and memory resources, as well as green LLM4SE solutions that reduce energy consumption, water usage, and carbon emissions. This paper aims to redirect the focus of the research community towards the efficiency and greenness of LLM4SE, while also sharing potential research directions to achieve this goal. It commences with a brief overview of the significance of LLM4SE and highlights the need for efficient and green LLM4SE solutions. Subsequently, the paper presents a vision for a future where efficient and green LLM4SE revolutionizes the LLM-based software engineering tool landscape, benefiting various stakeholders, including industry, individual practitioners, and society. The paper then delineates a roadmap for future research, outlining specific research paths and potential solutions for the research community to pursue. While not intended to be a definitive guide, the paper aims to inspire further progress, with the ultimate goal of establishing efficient and green LLM4SE as a central element in the future of software engineering.

  • 3 authors
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Apr 6, 2024

TestBench: Evaluating Class-Level Test Case Generation Capability of Large Language Models

Software testing is a crucial phase in the software life cycle, helping identify potential risks and reduce maintenance costs. With the advancement of Large Language Models (LLMs), researchers have proposed an increasing number of LLM-based software testing techniques, particularly in the area of test case generation. Despite the growing interest, limited efforts have been made to thoroughly evaluate the actual capabilities of LLMs in this task. In this paper, we introduce TestBench, a benchmark for class-level LLM-based test case generation. We construct a dataset of 108 Java programs from 9 real-world, large-scale projects on GitHub, each representing a different thematic domain. We then design three distinct types of prompts based on context descriptions, including self-contained context, full context, and simple context. Besides, we propose a fine-grained evaluation framework that considers five aspects of test cases: syntactic correctness, compilation correctness, test correctness, code coverage rate, and defect detection rate. Furthermore, we propose a heuristic algorithm to repair erroneous test cases generated by LLMs. We evaluate CodeLlama-13b, GPT-3.5, and GPT-4 on the TestBench, and our experimental results indicate that larger models demonstrate a greater ability to effectively utilize contextual information, thus generating higher-quality test cases. Smaller models may struggle with the noise introduced by the extensive information contained within the full context. However, when using the simplified version, namely the simple context, which is derived from the full context via abstract syntax tree analysis, the performance of these models improves significantly. Our analysis highlights the current progress and pinpoints future directions to further enhance the effectiveness of models by handling contextual information for test case generation.

  • 6 authors
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Sep 26, 2024

Bugs in Large Language Models Generated Code: An Empirical Study

Large Language Models (LLMs) for code have gained significant attention recently. They can generate code in different programming languages based on provided prompts, fulfilling a long-lasting dream in Software Engineering (SE), i.e., automatic code generation. Similar to human-written code, LLM-generated code is prone to bugs, and these bugs have not yet been thoroughly examined by the community. Given the increasing adoption of LLM-based code generation tools (e.g., GitHub Copilot) in SE activities, it is critical to understand the characteristics of bugs contained in code generated by LLMs. This paper examines a sample of 333 bugs collected from code generated using three leading LLMs (i.e., CodeGen, PanGu-Coder, and Codex) and identifies the following 10 distinctive bug patterns: Misinterpretations, Syntax Error, Silly Mistake, Prompt-biased code, Missing Corner Case, Wrong Input Type, Hallucinated Object, Wrong Attribute, Incomplete Generation, and Non-Prompted Consideration. The bug patterns are presented in the form of a taxonomy. The identified bug patterns are validated using an online survey with 34 LLM practitioners and researchers. The surveyed participants generally asserted the significance and prevalence of the bug patterns. Researchers and practitioners can leverage these findings to develop effective quality assurance techniques for LLM-generated code. This study sheds light on the distinctive characteristics of LLM-generated code.

  • 6 authors
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Mar 13, 2024

CodeRAG-Bench: Can Retrieval Augment Code Generation?

While language models (LMs) have proven remarkably adept at generating code, many programs are challenging for LMs to generate using their parametric knowledge alone. Providing external contexts such as library documentation can facilitate generating accurate and functional code. Despite the success of retrieval-augmented generation (RAG) in various text-oriented tasks, its potential for improving code generation remains under-explored. In this work, we conduct a systematic, large-scale analysis by asking: in what scenarios can retrieval benefit code generation models? and what challenges remain? We first curate a comprehensive evaluation benchmark, CodeRAG-Bench, encompassing three categories of code generation tasks, including basic programming, open-domain, and repository-level problems. We aggregate documents from five sources for models to retrieve contexts: competition solutions, online tutorials, library documentation, StackOverflow posts, and GitHub repositories. We examine top-performing models on CodeRAG-Bench by providing contexts retrieved from one or multiple sources. While notable gains are made in final code generation by retrieving high-quality contexts across various settings, our analysis reveals room for improvement -- current retrievers still struggle to fetch useful contexts especially with limited lexical overlap, and generators fail to improve with limited context lengths or abilities to integrate additional contexts. We hope CodeRAG-Bench serves as an effective testbed to encourage further development of advanced code-oriented RAG methods.

  • 7 authors
·
Jun 20, 2024

Leveraging Large Language Models for Generating Research Topic Ontologies: A Multi-Disciplinary Study

Ontologies and taxonomies of research fields are critical for managing and organising scientific knowledge, as they facilitate efficient classification, dissemination and retrieval of information. However, the creation and maintenance of such ontologies are expensive and time-consuming tasks, usually requiring the coordinated effort of multiple domain experts. Consequently, ontologies in this space often exhibit uneven coverage across different disciplines, limited inter-domain connectivity, and infrequent updating cycles. In this study, we investigate the capability of several large language models to identify semantic relationships among research topics within three academic domains: biomedicine, physics, and engineering. The models were evaluated under three distinct conditions: zero-shot prompting, chain-of-thought prompting, and fine-tuning on existing ontologies. Additionally, we assessed the cross-domain transferability of fine-tuned models by measuring their performance when trained in one domain and subsequently applied to a different one. To support this analysis, we introduce PEM-Rel-8K, a novel dataset consisting of over 8,000 relationships extracted from the most widely adopted taxonomies in the three disciplines considered in this study: MeSH, PhySH, and IEEE. Our experiments demonstrate that fine-tuning LLMs on PEM-Rel-8K yields excellent performance across all disciplines.

  • 4 authors
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Aug 28

Foundation Models and Fair Use

Existing foundation models are trained on copyrighted material. Deploying these models can pose both legal and ethical risks when data creators fail to receive appropriate attribution or compensation. In the United States and several other countries, copyrighted content may be used to build foundation models without incurring liability due to the fair use doctrine. However, there is a caveat: If the model produces output that is similar to copyrighted data, particularly in scenarios that affect the market of that data, fair use may no longer apply to the output of the model. In this work, we emphasize that fair use is not guaranteed, and additional work may be necessary to keep model development and deployment squarely in the realm of fair use. First, we survey the potential risks of developing and deploying foundation models based on copyrighted content. We review relevant U.S. case law, drawing parallels to existing and potential applications for generating text, source code, and visual art. Experiments confirm that popular foundation models can generate content considerably similar to copyrighted material. Second, we discuss technical mitigations that can help foundation models stay in line with fair use. We argue that more research is needed to align mitigation strategies with the current state of the law. Lastly, we suggest that the law and technical mitigations should co-evolve. For example, coupled with other policy mechanisms, the law could more explicitly consider safe harbors when strong technical tools are used to mitigate infringement harms. This co-evolution may help strike a balance between intellectual property and innovation, which speaks to the original goal of fair use. But we emphasize that the strategies we describe here are not a panacea and more work is needed to develop policies that address the potential harms of foundation models.

  • 6 authors
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Mar 27, 2023 1

MeSH Suggester: A Library and System for MeSH Term Suggestion for Systematic Review Boolean Query Construction

Boolean query construction is often critical for medical systematic review literature search. To create an effective Boolean query, systematic review researchers typically spend weeks coming up with effective query terms and combinations. One challenge to creating an effective systematic review Boolean query is the selection of effective MeSH Terms to include in the query. In our previous work, we created neural MeSH term suggestion methods and compared them to state-of-the-art MeSH term suggestion methods. We found neural MeSH term suggestion methods to be highly effective. In this demonstration, we build upon our previous work by creating (1) a Web-based MeSH term suggestion prototype system that allows users to obtain suggestions from a number of underlying methods and (2) a Python library that implements ours and others' MeSH term suggestion methods and that is aimed at researchers who want to further investigate, create or deploy such type of methods. We describe the architecture of the web-based system and how to use it for the MeSH term suggestion task. For the Python library, we describe how the library can be used for advancing further research and experimentation, and we validate the results of the methods contained in the library on standard datasets. Our web-based prototype system is available at http://ielab-mesh-suggest.uqcloud.net, while our Python library is at https://github.com/ielab/meshsuggestlib.

  • 3 authors
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Dec 18, 2022

Vibe Coding vs. Agentic Coding: Fundamentals and Practical Implications of Agentic AI

This review presents a comprehensive analysis of two emerging paradigms in AI-assisted software development: vibe coding and agentic coding. While both leverage large language models (LLMs), they differ fundamentally in autonomy, architectural design, and the role of the developer. Vibe coding emphasizes intuitive, human-in-the-loop interaction through prompt-based, conversational workflows that support ideation, experimentation, and creative exploration. In contrast, agentic coding enables autonomous software development through goal-driven agents capable of planning, executing, testing, and iterating tasks with minimal human intervention. We propose a detailed taxonomy spanning conceptual foundations, execution models, feedback loops, safety mechanisms, debugging strategies, and real-world tool ecosystems. Through comparative workflow analysis and 20 detailed use cases, we illustrate how vibe systems thrive in early-stage prototyping and education, while agentic systems excel in enterprise-grade automation, codebase refactoring, and CI/CD integration. We further examine emerging trends in hybrid architectures, where natural language interfaces are coupled with autonomous execution pipelines. Finally, we articulate a future roadmap for agentic AI, outlining the infrastructure needed for trustworthy, explainable, and collaborative systems. Our findings suggest that successful AI software engineering will rely not on choosing one paradigm, but on harmonizing their strengths within a unified, human-centered development lifecycle.

  • 3 authors
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May 25 2

ECtHR-PCR: A Dataset for Precedent Understanding and Prior Case Retrieval in the European Court of Human Rights

In common law jurisdictions, legal practitioners rely on precedents to construct arguments, in line with the doctrine of stare decisis. As the number of cases grow over the years, prior case retrieval (PCR) has garnered significant attention. Besides lacking real-world scale, existing PCR datasets do not simulate a realistic setting, because their queries use complete case documents while only masking references to prior cases. The query is thereby exposed to legal reasoning not yet available when constructing an argument for an undecided case as well as spurious patterns left behind by citation masks, potentially short-circuiting a comprehensive understanding of case facts and legal principles. To address these limitations, we introduce a PCR dataset based on judgements from the European Court of Human Rights (ECtHR), which explicitly separate facts from arguments and exhibit precedential practices, aiding us to develop this PCR dataset to foster systems' comprehensive understanding. We benchmark different lexical and dense retrieval approaches with various negative sampling strategies, adapting them to deal with long text sequences using hierarchical variants. We found that difficulty-based negative sampling strategies were not effective for the PCR task, highlighting the need for investigation into domain-specific difficulty criteria. Furthermore, we observe performance of the dense models degrade with time and calls for further research into temporal adaptation of retrieval models. Additionally, we assess the influence of different views , Halsbury's and Goodhart's, in practice in ECtHR jurisdiction using PCR task.

  • 3 authors
·
Mar 31, 2024

Pitfalls in Language Models for Code Intelligence: A Taxonomy and Survey

Modern language models (LMs) have been successfully employed in source code generation and understanding, leading to a significant increase in research focused on learning-based code intelligence, such as automated bug repair, and test case generation. Despite their great potential, language models for code intelligence (LM4Code) are susceptible to potential pitfalls, which hinder realistic performance and further impact their reliability and applicability in real-world deployment. Such challenges drive the need for a comprehensive understanding - not just identifying these issues but delving into their possible implications and existing solutions to build more reliable language models tailored to code intelligence. Based on a well-defined systematic research approach, we conducted an extensive literature review to uncover the pitfalls inherent in LM4Code. Finally, 67 primary studies from top-tier venues have been identified. After carefully examining these studies, we designed a taxonomy of pitfalls in LM4Code research and conducted a systematic study to summarize the issues, implications, current solutions, and challenges of different pitfalls for LM4Code systems. We developed a comprehensive classification scheme that dissects pitfalls across four crucial aspects: data collection and labeling, system design and learning, performance evaluation, and deployment and maintenance. Through this study, we aim to provide a roadmap for researchers and practitioners, facilitating their understanding and utilization of LM4Code in reliable and trustworthy ways.

  • 8 authors
·
Oct 27, 2023

From Copilot to Pilot: Towards AI Supported Software Development

AI-supported programming has arrived, as shown by the introduction and successes of large language models for code, such as Copilot/Codex (Github/OpenAI) and AlphaCode (DeepMind). Above human average performance on programming challenges is now possible. However, software engineering is much more than solving programming contests. Moving beyond code completion to AI-supported software engineering will require an AI system that can, among other things, understand how to avoid code smells, to follow language idioms, and eventually (maybe!) propose rational software designs. In this study, we explore the current limitations of AI-supported code completion tools like Copilot and offer a simple taxonomy for understanding the classification of AI-supported code completion tools in this space. We first perform an exploratory study on Copilot's code suggestions for language idioms and code smells. Copilot does not follow language idioms and avoid code smells in most of our test scenarios. We then conduct additional investigation to determine the current boundaries of AI-supported code completion tools like Copilot by introducing a taxonomy of software abstraction hierarchies where 'basic programming functionality' such as code compilation and syntax checking is at the least abstract level, software architecture analysis and design are at the most abstract level. We conclude by providing a discussion on challenges for future development of AI-supported code completion tools to reach the design level of abstraction in our taxonomy.

  • 2 authors
·
Mar 7, 2023

Using clarification questions to improve software developers' Web search

Context: Recent research indicates that Web queries written by software developers are not very successful in retrieving relevant results, performing measurably worse compared to general purpose Web queries. Most approaches up to this point have addressed this problem with software engineering-specific automated query reformulation techniques, which work without developer involvement but are limited by the content of the original query. In other words, these techniques automatically improve the existing query but can not contribute new, previously unmentioned, concepts. Objective: In this paper, we propose a technique to guide software developers in manually improving their own Web search queries. We examine a conversational approach that follows unsuccessful queries with a clarification question aimed at eliciting additional query terms, thus providing to the developer a clear dimension along which the query could be improved. Methods: We describe a set of clarification questions derived from a corpus of software developer queries and a neural approach to recommending them for a newly issued query. Results: Our evaluation indicates that the recommendation technique is accurate, predicting a valid clarification question 80% of the time and outperforms simple baselines, as well as, state-of-the-art Learning To Rank (LTR) baselines. Conclusion: As shown in the experimental results, the described approach is capable at recommending appropriate clarification questions to software developers and considered useful by a sample of developers ranging from novices to experienced professionals.

  • 2 authors
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Jul 26, 2022