Adapt Semantics, Not Structure: Few-Instance Schema Calibration for Scientific PDF Extraction

Enterprise workflows increasingly rely on agents for \emph{schema-guided extraction}: given a document and a user-defined schema, the agent faithfully follows the schema to produce the correct output with source evidence as grounding metadata. We present ExtractBench, a benchmark for schema-guided extraction and, to our knowledge, the first to score value accuracy, record completeness at scale, grounding, and measured cost together. The evaluation system contains 4,869 pages across 370 enterprise documents, 8 business domains, and 67 document types, with clear tags differentiating their challenge scenarios. The scalable schema and ground-truth curation pipeline combines independent-system agreement for real documents, known values for synthetic lists, and human verification for forms. We report order-insensitive value F1 for value accuracy, plus two grounding metrics for source traceability: word- and page-level F1. Commercial VLMs perform well on short documents but often truncate record lists on long ones, while coding agents retain higher accuracy at much higher cost. LlamaExtract Agentic Plus ranks first on all three metrics, with accuracy comparable to coding agents at a fraction of the cost. Dataset and evaluation code are available on \href{https://huggingface.co/datasets/llamaindex/ExtractBench}{HuggingFace} and \href{https://github.com/run-llama/ExtractBench}{GitHub}.

Extracting structured data from unstructured text using large language models (LLMs) becomes challenging when target schemas are large and complex. In such cases, including the full schema in the prompt increases cost and latency, risks lost-in-the-middle performance degradation, and can exceed context length limits. We propose SchemaRAG, a retrieval-augmented generation (RAG) framework that dynamically prunes the output schema space for schema-conditioned information extraction tasks by leveraging schema metadata and few-shot examples when available. We evaluate SchemaRAG on real-world healthcare and e-commerce datasets. Our results show that SchemaRAG can achieve up to an 8.8% increase in micro-F1, a 47% reduction in latency, and a 48% reduction in token costs, demonstrating its practicality for large-schema extraction.

Most methods that optimize LLM prompts and agent workflows assume that task-specific output schemas, extraction instructions, and evaluation criteria are predefined. For scientific extraction agents, however, a short task goal may not fully determine these components, while specifying them manually is costly. We study the upstream problem of constructing the task-specific configuration from a weak specification containing only a short goal and unannotated reference documents. Rather than treating automatic construction as a fixed preprocessing step, our framework constructs a task-specific schema, extraction instructions, and base training rubrics, then keeps schema construction and extraction instructions editable during optimization. Failure-focused updates concentrate textual-gradient feedback on lower-scoring documents, while training-time evaluation criteria adapt to recurring failures. On a heterogeneous-catalysis literature corpus, automatic construction remains improvable, and optimizing both schema construction and extraction instructions performs best across all four judge-rubric settings, with ablations and blinded human evaluation supporting the proposed formulation.