Reconnecting Fragmented Citation Networks with Semantic Augmentation

Vector search and retrieval-augmented generation (RAG) rest on the assumption that cosine similarity between text embeddings reflects conceptual relatedness. We measure where this assumption breaks. We build an augmented citation graph over 3.58M scientific papers and partition it via Leiden CPM at two granularities: sub-field (L1) and research-agenda (L2, hierarchical inside each L1). Four state-of-the-art embeddings (Gemini, Qwen3-8B, Qwen3-0.6B, SPECTER2) clear the L1 bar reasonably (45-52% top-10 same-rate) but stop working at L2: only 15-21% of top-10 neighbors share the query's research agenda. In absolute terms, 8 of every 10 retrieved papers are off-agenda. The failure is universal across eight scientific domains and all four models; SPECTER2, despite its citation-based contrastive training, is the weakest. As a diagnostic probe, we test whether the same augmented graph also functions as a retrieval signal: a deliberately simple citation-count rerank reaches 57.7% top-1 L2 on top of LLM-expanded Boolean retrieval and 59.6% on top of plain BM25, on 80 curated agenda queries -- about 9 points above the best cosine retriever (Gemini, 50.6%) and 20 points above BM25 alone (39.3%). The probe isolates a slice of the agenda-matching signal the graph carries but the embeddings miss, connecting recent theoretical limits on single-vector retrieval to a concrete failure mode of scientific RAG.

Knowledge graphs over corpora of inter-referencing documents - scholarly papers, legal opinions, policy briefs - encode the topology of reference but not its stance. The standard representation collapses a rich evaluative relation into an untyped edge, losing the very content that supports community-level queries about how one document is received by another. We propose the claim network: a representational pattern in which each cross-document reference is reified as a typed claim, carrying source, target, claim text, and a four-class stance label grounded in the citation-intent literature. We give a construction pipeline applicable to any corpus of scholarly inter-referencing documents and instantiate it on a corpus of 127 papers in 3D point cloud semantic segmentation, producing a network of 8,260 typed claims. Three downstream task families demonstrate what the network enables: retrieval signal augmentation, aggregated-stance summarisation, and topological analytics. Head-to-head evaluation against standard Retrieval-Augmented Generation (RAG) baselines shows that the gain over flat retrieval is the gain from the right intermediate representation rather than the wrong one.

Citation-based measures of scientific influence typically treat citations as uniform signals, ignoring the different roles that cited works play in a paper's contribution. We introduce contribution-based credit scoring for research articles: a structured citation analysis that decomposes a paper's credit between its own original contribution and the prior work it builds on. Motivated by a cooperative-game view of scientific credit, we propose the contribution tree, a hierarchical framework that conserves importance across the document structure and separates original from citation-derived contribution. To make this framework scalable, we use LLMs as noisy comparative estimators of local importance. We further extend the model to article collections by propagating contributions through weighted citation graphs, yielding corpus-level contributions and normalized influence scores. Our experiments suggest that our framework captures contribution signals beyond surface-level heuristics. Our code is available at https://github.com/sanaebrahimi/Importance_Scoring/