Do Agents Need a New Kind of Paper? SPRA: Structured Paper Representation for Agents

Scientific publication compresses a branching, iterative research process into a linear narrative, discarding the majority of what was discovered along the way. This compilation imposes two structural costs: a Storytelling Tax, where failed experiments, rejected hypotheses, and the branching exploration process are discarded to fit a linear narrative; and an Engineering Tax, where the gap between reviewer-sufficient prose and agent-sufficient specification leaves critical implementation details unwritten. Tolerable for human readers, these costs become critical when AI agents must understand, reproduce, and extend published work. We introduce the Agent-Native Research Artifact (ARA), a protocol that replaces the narrative paper with a machine-executable research package structured around four layers: scientific logic, executable code with full specifications, an exploration graph that preserves the failures compilation discards, and evidence grounding every claim in raw outputs. Three mechanisms support the ecosystem: a Live Research Manager that captures decisions and dead ends during ordinary development; an ARA Compiler that translates legacy PDFs and repos into ARAs; and an ARA-native review system that automates objective checks so human reviewers can focus on significance, novelty, and taste. On PaperBench and RE-Bench, ARA raises question-answering accuracy from 72.4% to 93.7% and reproduction success from 57.4% to 64.4%. On RE-Bench's five open-ended extension tasks, preserved failure traces in ARA accelerate progress, but can also constrain a capable agent from stepping outside the prior-run box depending on the agent's capabilities. Our code is open-sourced at https://github.com/Orchestra-Research/Agent-Native-Research-Artifact.

Current LLM-based research agents have advanced through agent orchestration, yet largely overlook scientific knowledge orchestration. Existing works often reduce papers to abstracts, surface mentions, and flat cites edges, omitting key entities, claims, evidence, mechanisms, and method lineages essential for scientific reasoning. To this end, we introduce Agents-K1, an end-to-end knowledge orchestration pipeline that converts raw documents into agent-native scientific knowledge graphs. Agents-K1 integrates three components under a unifying theoretical foundation: a multimodal parser whose five-module schema captures entities, multimodal evidence, citations, and typed inter-entity relations across the full paper rather than abstracts alone; a 4B information-extraction backbone trained with GRPO under a rule-based reward; and a graphanything CLI, a tri-source agent interface that unifies web search, multimodal graph retrieval, and cross-document traversal. On top of this, we process 2.46 million scientific papers across six subjects to produce Scholar-KG, of which we release a one-million-paper subset, and the full Scholar-KG is accessible via the SCP link below. The same pipeline can be extended to general-domain corpora and to schema-conformant data synthesis. Extensive experiments demonstrate that Agents-K1 achieves superior performance in scientific information extraction, knowledge graph construction, and multi-hop scientific reasoning.

What makes great scientists great? Even as AI systems start to make progress on open problems, scientists remain far ahead of them at sensing which prior idea, buried in an ever-growing archive of research, a new problem needs. To study this skill, we draw on researchers who know firsthand which earlier work advanced their completed projects, with papers serving as pointers to the ideas within. Using our automated pipeline that makes author annotation scalable, we build ScholarCatalyst by having 184 lead authors of 207 recent computer science papers label which candidates did or could have advanced their project, each with a detailed rationale. We introduce a retrieval task with author-provided judgments: given an initial research question, retrieve these papers from only the literature available when the project began. Agentic search does no better than embedding retrieval (0.42 vs. 0.48 Recall@20) despite calling that same retriever as a tool. Even an agent built on Claude Fable 5.1, which may have seen the completed papers during training, reaches only 0.51 R@20. These results highlight the need for new training recipes that equip models with expert intuition for searching broad corpora. We envision ScholarCatalyst as a step toward scientific agents that can take a half-formed idea and point to the prior research it needs.