Avatar: Toward Autonomous End-to-End Orchestration of Scientific Workflows using LLMs

Scientific workflow systems automate execution -- scheduling, fault tolerance, resource management -- but not the semantic translation that precedes it. Scientists still manually convert research questions into workflow specifications, a task requiring both domain knowledge and infrastructure expertise. We propose an agentic architecture that closes this gap through three layers: an LLM interprets natural language into structured intents (semantic layer); validated generators produce reproducible workflow DAGs (deterministic layer); and domain experts author ``Skills'': markdown documents encoding vocabulary mappings, parameter constraints, and optimization strategies (knowledge layer). This decomposition confines LLM non-determinism to intent extraction: identical intents always yield identical workflows. We implement and evaluate the architecture on the 1000 Genomes population genetics workflow and Hyperflow WMS running on Kubernetes. In an ablation study on 150 queries, Skills raise full-match intent accuracy from 44% to 83%; skill-driven deferred workflow generation reduces data transfer by 92%; and the end-to-end pipeline completes queries on Kubernetes with LLM overhead below 15 seconds and cost under $0.001 per query.

Large language model (LLM) agents are increasingly entrusted with natural-language workflow instructions (e.g., retail-payment policies) that specify not only what outcome to achieve, but also which steps, branches, and tool interactions are permitted. When these instructions are supplied as prompt context, however, the model retains control over both procedure selection and step execution. As interactions accumulate, an agent can skip required steps, take unsupported branches, or execute a valid step with unsupported arguments or effects--a failure mode we call workflow misalignment. In this work, we propose COVENANT, a compiler-and-interpreter architecture for workflow-aligned agent execution. Our key insight is to treat workflow instructions as source programs rather than prompts. COVENANT converts the instructions into a workflow abstract syntax tree (WAST) and lowers it to a workflow control-flow graph (WCFG). At runtime, a controller interprets the WCFG one node at a time, checks each proposal against requirements extracted from the instructions before committing controller state or advancing the graph, and returns diagnostic feedback for repair. To evaluate COVENANT, we use 120 cases from three existing benchmarks, spanning seven workflow scenarios. Compared with state-of-the-art LLM agents, COVENANT improves benchmark success from 50.00% to 83.33% and reduces the workflow-misalignment failure rate from 42.50% to 15.83% (62.75% relative). These results show that COVENANT substantially mitigates workflow misalignment, moving LLM-agent alignment beyond isolated prompt following toward reliable execution of complex and multi-step workflows.

Federated learning over medical images is a demanding workflow application. Each round fans out across parallel client jobs and converges on an aggregation step that feeds the next round. At scale this yields 101 sub-workflows and 2,679 jobs on GPUs at four sites, which takes an expert months to build, mostly on workflow mechanics rather than science. We ask how far AI assistance can automate such workflows. An LLM agent, grounded in a released plugin of Pegasus-specific skills, first produces a reviewable specification of checkable constraints and acceptance criteria, then generates the executable workflow. A validation loop repairs runtime failures, checks code against those constraints, and regenerates the implementation from the specification alone. We evaluate three LLM agents, report end-to-end runs on the FABRIC testbed, and show how conformance checking against the specification caught three silent errors that failure-driven debugging missed, including one that trained 1,700 jobs on random tensors.