DAGverse: Building Document-Grounded Semantic DAGs from Scientific Papers

Constructing causal directed acyclic graphs (DAGs) is a core step in biomedical causal analysis, yet it remains a largely manual process. Analysts must connect study variables to prior literature, evaluate uncertain causal claims, and preserve sufficient provenance for expert review. We present EviDAG, a browser-based system for authoring causal DAGs as auditable, evidence-linked artifacts from biomedical literature. Given free-text descriptions of study concepts, EviDAG creates a reproducible literature snapshot, uses an LLM-based reasoning module to generate structured pairwise causal judgments, links literature-supported judgments to verbatim evidence excerpts, and assembles the judgments into a constraint-checked graph. Each proposed edge includes confidence estimates, provenance, and a reviewable rationale. The interface supports study specification, progress monitoring, evidence review, graph comparison, adjustment-set computation, and export. In evaluations against both compact benchmark DAGs and reference DAGs derived from published literature, EviDAG achieves high edge recall on the literature-based cohort while retaining verifiable evidence trails absent from LLM-only baselines. EviDAG thus reduces the burden of causal DAG curation while making the resulting assumptions auditable, supporting the design, analysis, and interpretation of biomedical studies.

Deep research tasks require agents to navigate large knowledge spaces, synthesize evidence across many sources, and adapt their plans as findings emerge. Directed acyclic graph (DAG)-based multi-agent systems suit this setting because they support parallel execution and isolate each sub-task within a focused dependency context. Yet existing DAG-based agents instantiate a task-level plan before execution and repair the graph only after failures or missing evidence are observed. This Plan-then-Patch strategy is brittle for deep research: the system commits most strongly when its evidence is weakest, and later revisions waste computation on branches that should not have been planned. We propose DAGent, a DAG-based multi-agent framework with Evaluate-then-Grow incremental planning: an Orchestrator grows the task graph one batch at a time, conditioning each expansion on confidence and uncertainty signals from completed nodes. A hierarchical context layer propagates compact QueryDocs by default while preserving full execution traces for on-demand recall. The recorded DAG topology admits structural RL signals that outcome-only recipes cannot define; DAGRPO, a GRPO adaptation, injects topology-conditioned credit on Executor rollouts and a structural compliance regularization on Orchestrator plans. Across BrowseComp-Plus, GAIA, and xbench-DeepSearch, DAGent surpasses the strongest open-source baseline by 5.3 / 5.8 / 2.0 points at the Qwen3-235B-A22B scale, and the lead replicates across four open-source backbones and extends to GPT-5 at 327K context. At the Qwen3-8B scale, DAGRPO improves over a same-budget outcome-only GRPO baseline by 3.0 average Pass@1 points. A same-architecture comparison shows that evidence-conditioned planning reaches higher accuracy at lower per-task token, tool-call, and step footprints than its Plan-then-Patch counterpart. Code: https://github.com/hanwenliu6825/DAGent

Scientific papers require models to integrate evidence across text, equations, figures, tables, code, and datasets while preserving its provenance. Beyond answer correctness, scientific reading requires verifiable outputs from operations such as evidence localization, definition extraction, and consistency checking. We introduce SciDocBench, a workflow-centered benchmark targeting these operations through 124 expert-authored and difficulty-screened questions across seven research-assistant capability groups, 19 subtasks, and five scientific domains. Each question is instantiated in four matched settings formed by pairing its bilingual variants with the All Images First and Markdown Interleaved document representations, yielding 496 evaluation instances. The strongest evaluated model, Claude-Opus-5, scores 62.6 out of 100, with remaining gaps in evidence localization, structured information extraction, cross-document synthesis, and robustness to document representation. To convert these diagnostics into scalable training signals, we introduce SciDocIR, a structured representation of scientific document objects, layout and cross-reference relations, and provenance. Using SciDocIR, we construct SciDocDataset, which contains 4K supervised fine-tuning instances and 10K reinforcement-learning instances, built on 14 verifiable training subtasks. Post-training Qwen3.6-27B on task-aligned data improves its SciDocBench score from 40.03 to 45.33 with supervised fine-tuning and to 45.74 with subsequent reinforcement learning. Both adapted models preserve DocVQA and InfoVQA performance and improve ChartQA accuracy over the original model by 0.80 and 3.40 points, respectively. Together, SciDocBench, SciDocIR, and SciDocDataset connect capability diagnosis with verifiable training-data construction for scientific-document assistants.