Agentic Workflows

Large language models (LLMs) can plan scientific workflows and generate code, but these capabilities do not specify how scientific state is validated, transferred and recorded across heterogeneous computational and experimental operations. Here we present El Agente Gráfico, a semantic execution runtime for scientific agents that uses typed execution graphs to enforce admissible scientific state transitions, record provenance and confine model judgement to explicit decision points. Using the same top-level LLM and task-specific rubrics on six university-level quantum chemistry exercises, El Agente Gráfico improved performance while reducing model cost by approximately 80% and wall-clock time by more than fourfold relative to our previous multi-agent architecture. Across ensemble spectroscopy and metal-organic framework (MOF) design, the runtime supported typed-state transfer, parallel execution and cross-session persistence. Open-ended studies of a disulfide redox mechanism and the vibrational hypothesis of olfaction required the agent to define the chemical scope and computational pathway of each investigation. A graph-construction skill distilled from these studies then enabled coding agents to author typed execution graphs for MOF literature mining. Together, these results show how typed execution graphs turn reusable procedural knowledge into scientific protocols that can be inspected, revised and transferred across computational and physical systems.

Generative AI is reshaping knowledge work, yet existing research focuses predominantly on software engineering and the natural sciences, with limited methodological exploration for the humanities and social sciences. Positioned as a "methodological experiment," this study proposes an AI Agent-based collaborative research workflow (Agentic Workflow) for humanities and social science research. Taiwan's Claude.ai usage data (N = 7,729 conversations, November 2025) from the Anthropic Economic Index (AEI) serves as the empirical vehicle for validating the feasibility of this methodology. This study operates on two levels: the primary level is the design and validation of a methodological framework - a seven-stage modular workflow grounded in three principles: task modularization, human-AI division of labor, and verifiability, with each stage delineating clear roles for human researchers (research judgment and ethical decisions) and AI Agents (information retrieval and text generation); the secondary level is the empirical analysis of AEI Taiwan data - serving as an operational demonstration of the workflow's application to secondary data research, showcasing both the process and output quality (see Appendix A). This study contributes by proposing a replicable AI collaboration framework for humanities and social science researchers, and identifying three operational modes of human-AI collaboration - direct execution, iterative refinement, and human-led - through reflexive documentation of the operational process. This taxonomy reveals the irreplaceability of human judgment in research question formulation, theoretical interpretation, contextualized reasoning, and ethical reflection. Limitations including single-platform data, cross-sectional design, and AI reliability risks are acknowledged.

Operational rigor determines whether human-agent collaboration succeeds or fails. Scientific data pipelines need the equivalent of DevOps -- SciOps -- yet common approaches fragment provenance across disconnected systems without transactional guarantees. DataJoint 2.0 addresses this gap through the relational workflow model: tables represent workflow steps, rows represent artifacts, foreign keys prescribe execution order. The schema specifies not only what data exists but how it is derived -- a single formal system where data structure, computational dependencies, and integrity constraints are all queryable, enforceable, and machine-readable. Four technical innovations extend this foundation: object-augmented schemas integrating relational metadata with scalable object storage, semantic matching using attribute lineage to prevent erroneous joins, an extensible type system for domain-specific formats, and distributed job coordination designed for composability with external orchestration. By unifying data structure, data, and computational transformations, DataJoint creates a substrate for SciOps where agents can participate in scientific workflows without risking data corruption.

To address the reusability dilemma'' and structural hallucinations in enterprise Agentic AI,this paper proposes ReusStdFlow, a framework centered on a novel Extraction-Storage-Construction'' paradigm. The framework deconstructs heterogeneous, platform-specific Domain Specific Languages (DSLs) into standardized, modular workflow segments. It employs a dual knowledge architecture-integrating graph and vector databases-to facilitate synergistic retrieval of both topological structures and functional semantics. Finally, workflows are intelligently assembled using a retrieval-augmented generation (RAG) strategy. Tested on 200 real-world n8n workflows, the system achieves over 90% accuracy in both extraction and construction. This framework provides a standardized solution for the automated reorganization and efficient reuse of enterprise digital assets.

LLM agents execute multi-step workflows that mutate external state through tools. Common orchestrators treat tool return as the settlement trigger, so faults, speculation, and concurrent agents can leave partial effects, losing-branch residue, stale writes, or irreversible sends. Correct settlement needs two facts that retries, checkpoint replay, locks, and compensation each conflate: which effects must settle together, and when earlier conflicting work is exhausted. Atomix makes this split explicit with progress-aware transactions. The runtime records reads and effects during execution, seals a transaction when its footprint is complete, and commits only after per-resource frontiers show that no earlier conflicting work can still arrive. Commit is final settlement: Atomix releases bufferable effects, accepts reversible external effects as final, and lets irreversible effects leave the gate. Abort suppresses unreleased effects and compensates externalized reversible effects where possible. On representative agent workloads, this composition improves clean recovery under injected faults, isolates contending and speculative work, and prevents correctly classified irreversible actions from leaking; microbenchmarks show microsecond-scale wrapper overhead relative to tool latency.

LLM-driven agentic applications automate complex, multi-step tasks, but serving them efficiently remains difficult due to heterogeneous components, dynamic model-driven control flow, long-lived state, and highly variable latencies. Nalar is a serving framework for agent workflows that separates workflow specification from execution while providing the runtime visibility and control needed for robust performance. Nalar preserves ordinary Python interfaces and control flow through lightweight auto-generated stubs that turn agent and tool invocations into futures carrying dependency and execution-context metadata. A two-level control architecture combines global policy computation with local event-driven enforcement to support adaptive routing, scheduling, and resource management across evolving workflows. A workflow-aware KV-cache layer enables the runtime to manage cache placement and lifetime. Together, these mechanisms enable scalable, efficient, policy-driven serving of heterogeneous agentic applications without burdening developers with orchestration logic. Across three agentic workloads, Nalar reduces tail latency by 34-74% and achieves up to 3.38x speedups.

We present the first language-model-driven agentic artificial intelligence (AI) system to autonomously execute multi-stage physics experiments on a production synchrotron light source. Implemented at the Advanced Light Source particle accelerator, the system translates natural language user prompts into structured execution plans that combine archive data retrieval, control-system channel resolution, automated script generation, controlled machine interaction, and analysis. In a representative machine physics task, we show that preparation time was reduced by two orders of magnitude relative to manual scripting even for a system expert, while operator-standard safety constraints were strictly upheld. Core architectural features, plan-first orchestration, bounded tool access, and dynamic capability selection, enable transparent, auditable execution with fully reproducible artifacts. These results establish a blueprint for the safe integration of agentic AI into accelerator experiments and demanding machine physics studies, as well as routine operations, with direct portability across accelerators worldwide and, more broadly, to other large-scale scientific infrastructures.

Agentic Software Engineering (SE 3.0) represents a new era where intelligent agents are tasked not with simple code generation, but with achieving complex, goal-oriented SE objectives. To harness these new capabilities while ensuring trustworthiness, we must recognize a fundamental duality within the SE field in the Agentic SE era, comprising two symbiotic modalities: SE for Humans and SE for Agents. This duality demands a radical reimagining of the foundational pillars of SE (actors, processes, tools, and artifacts) which manifest differently across each modality. We propose two purpose-built workbenches to support this vision. The Agent Command Environment (ACE) serves as a command center where humans orchestrate and mentor agent teams, handling outputs such as Merge-Readiness Packs (MRPs) and Consultation Request Packs (CRPs). The Agent Execution Environment (AEE) is a digital workspace where agents perform tasks while invoking human expertise when facing ambiguity or complex trade-offs. This bi-directional partnership, which supports agent-initiated human callbacks and handovers, gives rise to new, structured engineering activities (i.e., processes) that redefine human-AI collaboration, elevating the practice from agentic coding to true agentic software engineering. This paper presents the Structured Agentic Software Engineering (SASE) vision, outlining several of the foundational pillars for the future of SE. The paper culminates in a research roadmap that identifies a few key challenges and opportunities while briefly discussing the resulting impact of this future on SE education. Our goal is not to offer a definitive solution, but to provide a conceptual scaffold with structured vocabulary to catalyze a community-wide dialogue, pushing the SE community to think beyond its classic, human-centric tenets toward a disciplined, scalable, and trustworthy agentic future.