Large Language Models (LLMs) offer new possibilities for scaling qualitative analysis, but existing applications often provide limited methodological transparency regarding how qualitative methods are translated into computational procedures. This paper presents an auditable and privacy-preserving computational operationalization of inductive and latent Thematic Analysis (TA). This paper first derives five design principles from the methodological requirements of TA and the conditions introduced by LLM-based inference: preserving interpretative context, maintaining traceable relationships between empirical material and analytical outputs, representing analytical constructs and reasoning explicitly, constraining LLM inference to interpretative tasks, and enabling privacy-preserving local deployment. Second, it presents a proof-of-concept for a two-phase workflow that operationalizes these principles by combining interpretative LLM inference with deterministic procedural control to generate codes, analytical justifications, themes, and theme descriptions while preserving explicit links to the source material. Third, it proposes an evaluation framework combining structural comparison with human-led TA and independent expert assessment of analytical quality. The evaluation is conducted on semi-structured Danish interview transcripts. and the results shows that the workflow produces code-level outputs with coverage broadly comparable to human annotations and highly rated analytical justifications, while generating a more compressed thematic structure characterized by fewer and broader themes. The findings demonstrate the feasibility of auditable LLM-supported TA through a modular workflow designed to scale to larger datasets, accommodate different LLMs, and support transfer across research domains, with domain adaptation primarily requiring adjustments to the prompting strategy.
This paper addresses the recovery of essay-scale republication and reuse from fragmented text-reuse evidence, a setting whose central challenge is pair-level evidence consolidation and not fragment retrieval alone. The study focuses on a candidate set centered on essays by eighteenth-century Scottish philosopher David Hume, spanning books from ECCO (Eighteenth Century Collections Online) and historical newspapers. Because the input consists of fragmented reuse hits instead of clean document pairs, and positive coverage is inherently incomplete, we formulate the task as pair-level evidence consolidation into plausible transmission relations and compare three methodological families: a staged rule-based workflow, baselines (a decision tree and two direct LLM settings), and automated rule adaptation. On labeled ECCO--ECCO slices, pair-level feature aggregation alone already reaches 0.948 F1 on the main labeled slice, while the final workflow gives the strongest overall precision-recall trade-off among the tested rule stages. On the full ECCO--ECCO candidate universe, direct LLM baselines flag up to 14,886 pairs as reprints compared to 771 for the final workflow, behaving in this direct-prompt setup as high-recall candidate expanders rather than precision-controlled deployment classifiers. On ECCO--Newspaper, manual audit confirms all 176 predicted positives as genuine cases of republication or reuse, while issue duplication and source-side multiplicity reveal additional provenance structure. Under incomplete ground truth, auditable pair-level evidence consolidation provides a practical way to produce compact candidate spaces for historical inspection.
Turning a research idea into a complete paper requires more than text generation: the system must retrieve literature, design and execute experiments, revise claims according to evidence, produce publication-ready figures, and maintain consistency across a long generation process. We present Spark-to-Paper, an end-to-end research paper generation system implemented as thirteen composable skills inside an existing coding assistant, without requiring a separate agent platform or orchestration service. Spark-to-Paper separates model-based judgment from deterministic operations that can be directly executed and checked. It further separates experiment planning from reporting, so that required evidence is specified before results are observed and manuscript claims are revised according to measured outcomes. To improve reliability over long research trajectories, the system combines deterministic integrity checks with self-critique and bounds a failure mode we call the Self-Refutation Loop, in which repeated experiments continue to reject the original research objective. Spark-to-Paper also produces editable vector figures through programmatic plotting for experimental results and code-based reconstruction for generated method diagrams. Across eight controlled research topics, Spark-to-Paper achieves 99.5% citation validity and 96.4% figure editability. A controlled ablation increases fabrication detection from 14% for a single-pass draft to 92% with the full integrity and review stack, while adversarial review achieves 74% precision. The full system uses 11.9M tokens, costs $8.1 per manuscript, and requires 3.2 hours on average. These results show that end-to-end research paper generation can be implemented as a lightweight, composable workflow inside existing coding assistants while keeping experimental evidence central to how claims are accepted, revised, or abandoned.
Memory is essential as language agents move from isolated tasks to long-horizon, stateful workflows, yet existing evaluations often reduce it to retrieval or question answering. We introduce ContextWeave, a longitudinal benchmark that evaluates whether recalled experience improves downstream agent performance in realistic office-work streams. ContextWeave reconstructs privacy-preserved, multi-month workflows of 14 participants into 1,005 executable tasks, including 568 core evaluation tasks, with instructions, containerized environments, trajectories, and task-specific rubrics. It measures workspace quality and alignment with participant-specific preferences, complemented by diagnostics of relevance, continuity, solvability, and robustness to misleading recall. Across six memory components under a fixed model, the strongest configuration raises Workspace Score from 68.08 to 78.20 and Preference Score from 41.50 to 70.60. With a fixed memory component, recall improves both outcomes for all five tested base models, although gains vary substantially. Our analysis shows that actionable, experience-rich memory supports workflow continuation and reduces redundant exploration more effectively than compact summaries, while it can also be more susceptible to misleading recall. These findings motivate memory systems that optimize not only retrieval relevance but also reliable use during execution.
Constantin Dalyac, Alexandre Dauphin, Loïc Henriet +1quant-ph cond-mat.quant-gas cs.AI
Quantum computers are moving from research laboratories to industrial machines accessible via the cloud and integrated into high-performance computing facilities. However, translating theoretical quantum protocols into hardware experiments remains a major bottleneck, requiring expertise across protocol design, compilation, simulation, and cloud execution. Here, we introduce an agentic workflow that automates this pipeline on neutral-atom quantum processors (here two Pasqal QPUs available on the cloud) while keeping the researcher in the loop for critical validation. In three case studies from many-body physics and optimization, the agent went from published paper or patent to a QPU campaign run overnight. In particular, human intervention was crucial to ensure scientific validity: the agent selected an inadequate observable in one experiment and constructed a plausible but incorrect hardware diagnosis in another, with both failures detected only through domain-expert review. Finally, we use a second agent to classify a corpus of 633 Rydberg-array arXiv papers and show that nearly half are implementable on present-day QPUs while identifying specific hardware upgrades needed for the rest. Together, these results demonstrate that agentic workflows provide a practical bridge between theoretical ideas and physical hardware, opening quantum experimentation to a much broader scientific community.
Recent work has explored the use of Large Language Models (LLMs) to automate simulation model building, typically by generating executable code directly from natural language descriptions. However, this raises challenges for verification and reproducibility particularly for users without programming expertise. We propose Sketch2DES, a sketch-to-simulation workflow that converts diagrammatic representations of queuing networks into verifiable discrete-event simulation models using open-weight LLMs. The workflow has three stages: (1) translation of a diagram into a semi-structured textual description using a multimodal LLM; (2) conversion into schema-validated structured data (JSON) via an LLM with a reflection-based verification loop; and (3) deterministic transformation into an executable simulation model using a software adapter. Intermediate artefacts can therefore be inspected and automatically validated before execution. We evaluate the approach on eight queuing-network diagrams of varying complexity. The workflow achieved high reliability for all stages, and results were statistically indistinguishable from human-coded and analytical benchmarks. Compared to direct code generation, the workflow improves reproducibility, transparency, and verifiability, while reducing the need for programming expertise. Limitations include restricted model scope and dependence on accurate visual interpretation. The results demonstrate the feasibility of structured, workflow-based model generation as a robust foundation for LLM-assisted simulation modelling.
Scientific machine learning papers typically make computational claims, e.g., that the relative mean square error is less than 5% or that the 95% predictive credible interval covers the test data. A coding agent can be prompted to replicate those claims from paper materials alone, but the prompt does not by itself reliably preserve progress or check whether generated evidence supports the paper's claims. We introduce Paper-replication, a workflow that makes each selected paper claim a target with recorded evidence, and implement it as a coding-agent skill. The workflow makes the agent record those targets, reconstruct the paper's method, run computational experiments, link generated outputs to provenance and comparisons with the paper's claims, record where matched evidence appears in the replication report, and pass validation checks before completion. We evaluate Paper-replication on twelve independent runs across four scientific machine learning papers. All twelve workspaces pass the completion gate, and all 158 recorded targets are matched with report coverage. Even in this completed workspace state, repeated runs differ in how papers are divided into targets, in numerical fidelity to the source papers, in elapsed replication time, in the number of intermediate executions replaced before final evidence is accepted, and in the rules used to accept evidence. Paper-replication makes completion depend on workspace evidence and validation checks rather than on the agent's final message.
Interactive visualizations support conceptual understanding in undergraduate mathematics, but building them has required programming expertise most instructors lack. Using a design-based research approach, we develop, deploy, and evaluate a six-phase workflow (Foundation, Customization, Mathematical Depth, Application, Accessibility, Pedagogical Control) that uses generative AI to build WCAG~2.2 Level~AA compliant visualizations without programming. The six phases structure every prompt, scaffold the AI's code generation, and define where human verification is applied. We ask whether the structure reliably yields correct and accessible tools, whether it runs both backward (reverse-engineering prompts from a finished tool) and forward (generating a tool from a plain-language idea), and what verification each phase requires. Across four deployed tools spanning calculus, multivariable calculus, and differential equations, we evaluate mathematical correctness against closed forms, accessibility through automated and manual screen-reader testing, and the errors that recurred. The structure produces structurally complete first-pass tools, but human verification remains mandatory at every phase: each output must be checked for mathematical correctness, accessibility, and pedagogical fit before the next phase begins. The workflow is platform-independent and serves both instructors and students.
We introduce the process harness, a new mechanism for uplifting legacy workflows into Agentic Business Process Management (Agentic BPM) without replacing the underlying workflow engine. A process harness places a policy-governed agentic layer around a deterministic workflow engine, intercepting designated control points to contribute reasoning, adaptation, and oversight while the engine retains structural authority over the process. To define the process harness rigorously, we develop the Task-Decision-Flow (TDF) model, specifying both its data schema and its execution semantics. TDF decomposes LLM reasoning across three policy-governed agent types: a TaskAgent for knowledge-intensive task execution, a DecisionAgent for per-case gateway routing, and a FlowAgent that governs runtime flow adaptation through a principled hook mechanism. Each agent reasons within an explicit policy drawn from the process FRAME, the aggregate policy set governing all LLM calls in the system. We then present CUGA FLO as the design and implementation realization of the TDF model, and demonstrate it on a loan approval workflow that exercises all three agent types and hook-driven regulatory override. The process harness uniquely reconciles imperative requirements, realized through deterministic workflow execution that enforces structural compliance, with normative requirements, realized through policy-framed agentic autonomy invoked at designated control points wherever the process demands it.
Woong Shin, Craig A. Bridges, Marshall T. McDonnell +1cs.AI
As scientific workflows shift from deterministic executables to LLM-based agents, the development practices on offer, such as fine-tuning, reinforcement learning, and prompt-and-go, bury the scientist's judgment. We propose treating agent construction as a workflow stage and introduce AgentBuild, which builds a scientific agent from a contract the scientist authors. The contract is a version-controlled rubric, a difficulty-graded curriculum, and a curated external knowledge base. A rubric-driven judge gates a meta-optimizer coding agent that edits the agent within a declared boundary, so the build compiles the agent, not the scientist's judgment. We instantiate this for Rietveld refinement of X-ray diffraction data through GSAS-II behind MCP and A2A, where a blank-harness construction run progresses through a lithium lanthanum zirconium oxide (LLZO) signal-to-noise ladder, reaches the 4 hour scan as a frontier case, and exposes the workflow-scope limits that remain. The same rubric that rewards credible fits also scores trajectory scope, making the frontier a contract failure rather than a pattern-fitting failure. As base models evolve, re-running AgentBuild is a re-tune, not a rebuild, and the scientist's authored contract remains the durable asset.
Financial-research answers are decision-relevant only when another analyst can audit how they were produced: which source was chosen, which period and accounting definition were used, which assumptions were made, and how the calculation was performed. Existing finance benchmarks largely evaluate isolated subskills or final answers, leaving the auditable derivation itself under-measured. We introduce BigFinanceBench, a 928-item expert-authored benchmark of open-ended financial-research tasks in which each item pairs a ground-truth reference answer with a point-weighted rubric that decomposes the derivation into independently checkable steps. BigFinanceBench is workflow-grounded in that it evaluates the full derivation rather than only the final output. Across 36,241 rubric points, the benchmark supports partial-credit evaluation and localization of failures across the analyst workflow. Evaluating ten current frontier and open-weight agents, we find substantial headroom: the best system reaches only 58.8% rubric score, final-answer accuracy is a useful but lossy proxy for derivation quality, and model capability varies non-uniformly across financial workflows.
Recent advances in large language models (LLMs) have opened up new possibilities for automated document formatting. However, real-world formatting often requires identifying targets based on document content. This content-aware setting remains challenging and underexplored, primarily due to the lack of dedicated evaluation datasets.To enable evaluation in realistic content-aware scenarios, we introduce DocFormBench, a benchmark that extends Text-to-Format evaluation to diverse formatting requirements, along with metrics for both accuracy and efficiency.To mitigate redundant document reading in existing methods during formatting, we propose DocFormFlow, a workflow formatting method that decouples target localization from modification execution into what to format and how. Extensive experiments across multiple LLMs and multimodal models show that DocFormFlow consistently improves formatting accuracy while reducing token consumption compared to representative baselines. Further analysis reveals that precise target localization is the primary factor influencing formatting performance. We hope DocFormBench and DocFormFlow will facilitate future research toward more intelligent and reliable document formatting.
Scientists increasingly rely on sensor-based data; however transforming raw streams into insights across the edge-to-cloud continuum remains difficult due to the breadth of expertise required to coordinate the necessary data and computation flow. This paper introduces a pattern-based, AI-assisted methodology for rapid development of sensor-driven applications. Using Pegasus workflows executing on the FABRIC testbed, we demonstrate a 5-step development loop that shifts workflow construction and deployment from code-first to intent-first design. Starting from an existing Orcasound hydrophone workflow as a reusable template, we generate and refine workflows for air quality, earthquake, and soil moisture monitoring applications. We further show how these workflows extend to edge resources-including BlueField-3 DPUs and Raspberry Pis-through configuration and placement rather than workflow redesign. Our evaluation, from the perspective of a novice Pegasus user, shows that AI-assisted pattern reuse compresses multi-stage workflow development to 1-1.5 days per workflow while preserving the rigor and portability of workflow-based execution.
Even Eilertsen, Vasileios Mavroeidis, Gudmund Grovcs.CR cs.AI
Security analysts are overwhelmed by the volume of alerts and the low context provided by many detection systems. Early-stage investigations typically require manual correlation across multiple log sources, a task that is usually time-consuming. In this paper, we present an experimental, agentic workflow that leverages large language models (LLMs) augmented with predefined queries and constrained tool access (structured SQL over Suricata logs and grep-based text search) to automate the first stages of alert investigation. The proposed workflow integrates queries to provide an overview of the available data, and LLM components that selects which queries to use based on the overview results, extracts raw evidence from the query results, and delivers a final verdict of the alert. Our results demonstrate that the LLM-powered workflow can investigate log sources, plan an investigation, and produce a final verdict that has a significantly higher accuracy than a verdict produced by the same LLM without the proposed workflow. By recognizing the inherent limitations of directly applying LLMs to high-volume and unstructured data, we propose combining existing investigation practices of real-world analysts with a structured approach to leverage LLMs as virtual security analysts, thereby assisting and reducing the manual workload.