AI-Assisted Software Development

We present spectroxide, a code package for computing cosmic microwave background spectral distortions in which all ${\sim}14{,}500$ lines of Rust code, Python interface, and ${\sim}400$ automated tests were written by an AI assistant (Claude Code) under human physicist supervision. The solver evolves the photon Boltzmann equation under Compton scattering, double Compton emission, and Bremsstrahlung from $z \sim 5 \times 10^6$ to the present, computing spectral distortions from arbitrary heat and photon injection within this redshift range. No fully open-source code of this kind is publicly available; we validate against analytic limits, published spectra, and publicly available precomputed Green's function tables. We document the development as a case study in AI-assisted scientific computing, highlighting how domain expertise caught physics bugs (incorrect dimensional prefactors, near-cancellation errors) that evaded the full automated test suite, and provide recommendations for best practices in human--AI collaborative development of scientific software. We make spectroxide publicly available on GitHub.

Software documentation frequently becomes outdated or fails to exist entirely, yet developers need focused views of their codebase to understand complex systems. While automated reverse engineering tools can generate UML diagrams from code, they produce overwhelming detail without considering developer intent. We introduce query-driven UML diagram generation, where LLMs create diagrams that directly answer natural language questions about code. Unlike existing methods, our approach produces semantically focused diagrams containing only relevant elements with contextual descriptions. We fine-tune Qwen2.5-Coder-14B on a curated dataset of code files, developer queries, and corresponding diagram representations in a structured JSON format, evaluating with both automatic detection of structural defects and human assessment of semantic relevance. Results demonstrate that fine-tuning on a modest amount of manually corrected data yields dramatic improvements: our best model achieves the highest F1 scores while reducing defect rates below state-of-the-art LLMs, generating diagrams that are both structurally sound and semantically faithful to developer queries. Thus, we establish the feasibility of using LLMs for scalable contextual, on-demand documentation generation. We make our code and dataset publicly available at https://github.com/i-need-a-pencil/query2diagram.

Code review is central to software engineering education but hard to scale in capstone projects due to tight deadlines, uneven peer feedback, and limited prior experience. We investigate an LLM-as-reviewer integrated directly into GitHub pull requests (human-in-the-loop) across two cohorts (more than 100 students, 2023--2024). Using a mixed-methods design -- GitHub data, reflective reports, and a targeted survey -- we examine engagement and responsiveness as behavioral indicators of self-regulated learning processes. Quantitatively, the 2024 cohort produced more iterative activity (1176 vs. 581 PRs), while technical issues observed in 2023 (227 failed AI attempts) dropped to zero after tool and instructional refinements. Despite different adoption levels (93% vs. 50% of teams using the tool), responsiveness was stable: 32% (2023) and 33% (2024) of successfully AI-reviewed PRs were followed by subsequent commits on the same PR. Qualitatively, students used the LLM's structured comments to focus reviews and discuss code quality, while guidance reduced over-reliance. We contribute: (i) an in-workflow design for an AI reviewer that scaffolds learning while mitigating cognitive offloading; (ii) a repeated cross sectional comparison across two cohorts in authentic settings; (iii) a mixed-methods analysis combining objective GitHub metrics with student self-reports; and (iv) evidence-based pedagogical recommendations for responsible, student-led AI-assisted review.

The capabilities of AI-assisted coding are progressing at breakneck speed. Chat-based vibe coding has evolved into fully fledged AI-assisted, agentic software development using agent scaffolds where the human developer creates a plan that agentic AIs implement. One current trend is utilizing documents beyond this plan document, such as project and method-scoped documents. Here we propose GROUNDING$.$md, a community-governed, field-scoped epistemic grounding document, using mass spectrometry-based proteomics as an example. This explicit field-scoped grounding document encodes Hard Constraints (non-negotiable validity invariants empirically required for scientific correctness) and Convention Parameters (community-agreed defaults) that override all other contexts to enforce validity, regardless of what the user prompts. In practice, this will empower a non-domain expert to generate code, tools, and software that have best practices baked in at the ground level, providing confidence to the software developer but also to those reviewing or using the final product. Undoubtedly it is easier to have agentic AIs adhere to guidelines than humans, and this opportunity allows for organizations to develop epistemic grounding documents in such a way as to keep domain experts in the loop in a future of democratized generation of bespoke software solutions.

Generative AI (GenAI) is reshaping software engineering by shifting development from manual coding toward agent-driven implementation. While vibe coding promises rapid prototyping, it often suffers from architectural drift, limited traceability, and reduced maintainability. Applying the design science research (DSR) methodology, this paper proposes Shift-Up, a framework that reinterprets established software engineering practices, like executable requirements (BDD), architectural modeling (C4), and architecture decision records (ADRs), as structural guardrails for GenAI-native development. Preliminary findings from our exploratory evaluation compare unstructured vibe coding, structured prompt engineering, and the Shift-Up approach in the development of a web application. These findings indicate that embedding machine-readable requirements and architectural artifacts stabilizes agent behavior, reduces implementation drift, and shifts human effort toward higher-level design and validation activities. The results suggest that traditional software engineering artifacts can serve as effective control mechanisms in AI-assisted development.

Developing Visual Analytics (VA) applications requires integrating complex machine learning models with expressive interactive interfaces. Developers face a stark trade-off: building tightly-coupled monoliths plagued by fragile interdependencies, or relying on restrictive, simplistic frameworks. Meanwhile, unconstrained, single-shot AI code generation promises speed but yields unstructured, unauditable chaos. The core challenge is combining the control and expressiveness of custom development with the efficiency of AI generation under strict constraints. To address this, we introduce BONSAI, a mixed-initiative workspace for the multi-agent co-development of VA applications. BONSAI utilizes a modular four-layer architecture (hardware, services, orchestration, application) that allows human and AI developers to independently contribute reusable components. The workspace incorporates this architecture into a structured four-phase development process (plan, design, monitor, and review), ensuring distributed agency and full provenance, where all human and AI contributions are structurally bounded and tracked. We evaluate BONSAI through case studies demonstrating the efficient creation of novel tools and the rapid reconstruction of complex VA applications directly from research paper descriptions. Ultimately, this paper contributes a conceptual workflow, a scalable architecture, and an integrated system that successfully balances AI's generative speed with the structural rigor required for complex VA development.

Current AI-assisted programming tools are predominantly linear and chat-based, which deviates from the iterative and branching nature of programming itself. Our preliminary study with developers using AI assistants suggested that they often struggle to explore alternatives, manage prompting sequences, and trace changes. Informed by these insights, we created EvoGraph, an IDE plugin that integrates AI interactions and code changes as a lightweight and interactive development graph. EvoGraph automatically records a branching AI-assisted coding history and allows developers to manipulate the graph to compare, merge, and revisit prior collaborative AI programming states. Our user study with 20 participants revealed that EvoGraph addressed developers' challenges identified in our preliminary study while imposing lower cognitive load. Participants also found the graph-based representation supported safe exploration, efficient iteration, and reflection on AI-generated changes. Our work highlights design opportunities for tools to help developers make sense of and act on their problem-solving progress in the emerging AI-mediated programming context.

This paper presents a controlled quasi-experimental developer study examining whether a layer-based security training package is associated with improved security quality in LLM-assisted implementation of an identity-centric Java Spring Boot backend. The study uses a mixed design with a within-subject pre-training versus post-training comparison and an exploratory between-subject expertise factor. Twelve developers completed matched runs under a common interface, fixed model configuration, counterbalanced task sets, and a shared starter project. Security outcomes were assessed via independent manual validation of submitted repositories by the first and second authors. The primary participant-level endpoint was a severity-weighted validated-weakness score. The post-training condition showed a significant paired reduction under an exact Wilcoxon signed-rank test ($p = 0.0059$). In aggregate, validated weaknesses decreased from 162 to 111 (31.5%), the severity-weighted burden decreased from 432 to 267 (38.2%), and critical findings decreased from 24 to 5 (79.2%). The largest reductions were in authorization and object access (53.3%) and in authentication, credential policy, and recovery weaknesses (44.7%). Session and browser trust-boundary issues showed minimal change, while sensitive-data and cryptographic weaknesses showed only marginal improvement. These results suggest that, under the tested conditions, post-training runs reduce validated security burden in LLM-assisted backend development without modifying the model. They do not support replacing secure defaults, static analysis, expert review, or operational hardening.

AI-based systems, currently driven largely by LLMs and tool-using agentic harnesses, are increasingly discussed as a possible threat to software engineering. Foundation models get stronger, agents can plan and act across multiple steps, and tasks such as scaffolding, routine test generation, straightforward bug fixing, and small integration work look more exposed than they did only a few years ago. The result is visible unease not only among students and junior developers, but also among experienced practitioners who worry that hard-won expertise may lose value. This paper argues for a different reading. The important shift is not that software engineering loses relevance. It is that the thing being engineered expands beyond executable code to semi-executable artifacts; combinations of natural language, tools, workflows, control mechanisms, and organizational routines whose enactment depends on human or probabilistic interpretation rather than deterministic execution. The Semi-Executable Stack is introduced as a six-ring diagnostic reference model for reasoning about that expansion, spanning executable artifacts, instructional artifacts, orchestrated execution, controls, operating logic, and societal and institutional fit. The model helps locate where a contribution, bottleneck, or organizational transition primarily sits, and which adjacent rings it depends on. The paper develops the argument through three worked cases, reframes familiar objections as engineering targets rather than reasons to dismiss the transition, and closes with a preserve-versus-purify heuristic for deciding which legacy software engineering processes, controls, and coordination routines should be kept and which should be simplified or redesigned. This paper is a conceptual keynote companion: diagnostic and agenda-setting rather than empirical.

Multi-agent frameworks (MAFs) promise to simplify LLM-driven software development, yet no principled metric captures how well AI coding assistants can generate correct, framework-specific code. We introduce \textit{AI-assistability} ($\mathcal{AI}$), a composite metric that quantifies a framework's amenability to AI-assisted development by combining structural alignment ($\barσ$) with functional correctness (pass@1). To evaluate this metric in a controlled setting, we design DDL2PropBank, a novel benchmark task that maps relational database schemas to PropBank semantic rolesets, and implement identical agent logic across ten frameworks using the Agent-as-a-Tool pattern. Our results challenge the intuition that declarative framework design guarantees AI-assistability: Agno, with a single canonical pattern and convention-aligned API, achieves the highest $\mathcal{AI}$ score (0.55), while DSPy -- the most declarative framework by design -- scores lowest (0.07), as its novel abstractions are insufficiently represented in AI training data. We find that convention alignment, not declarative design alone, is the primary driver of AI-assistability ($r = 0.576$ between $\barσ$ and pass@1). All artifacts -- DDL2PropBank, PropBank MCP server, and all implementations -- are available at https://github.com/ahmeshaf/ddl2propbank