Quantum Knowledge Graph: Modeling Context-Dependent Triplet Validity

A recent Nature Medicine study reports that general-purpose frontier LLMs outperform specialized retrieval-augmented clinical tools on medical benchmarks, and that retrieval can hurt strong models. We ask the natural follow-up: does structured knowledge-graph (KG) grounding change this, and when does grounding help at all? We contribute two results. First, a reproduction: the study's headline HealthBench score (~88) is the Consensus variant, not full HealthBench, where frontier models and ideal completions both score ~46-47 under a physician-calibrated grader (agreement 82.5%); we reproduce GPT-5.2 Consensus =90.9 and flag a score-deflating grader bug. Second, a knowledge-boundary result. Using a graph+vector engine (samyama-graph) over the public biomedical KG PrimeKG, neither naive triple retrieval nor an agentic natural-language-to-Cypher loop (82% successful queries) improves MedQA across a weak-to-strong model ladder (all |Delta| <= 3.4). On a synthetic counterfactual KG, and on a hybrid benchmark mixing known and novel facts, the identical pipeline lifts out-of-training accuracy from chance to ~100% (+68 to +79) while adding nothing on known facts (a no-LLM arm answers both). Across three regimes (no-knowledge, graph-aided, hybrid), grounding helps only insofar as the decisive fact lies outside the model's training -- public-KG facts are redundant, private and novel data are where it pays -- matching the study's institutional-data caveat.

Question-answering often requires reasoning across multiple connected facts rather than retrieving a single isolated relation. Knowledge graphs (KGs) provide a structured way to represent such facts, but training large language models (LLMs) only on isolated KG head-relation-tail triples may limit their ability to learn the surrounding context needed for multi-hop reasoning. In this work, we propose a context-augmented training framework for multi-hop question-answering. Although generally applicable, we validate the framework in the context of disease-specific KGs, extracted using a reliable KG extraction framework called GraphMERT, for Gastroparesis and Diabetes. For each primary KG triple, we attach supporting triples extracted from the same source text chunk to form a context graph (CG). This creates two supervision settings: KG-grounded supervision, which uses only the target KG triple or path, and CG-grounded supervision, which uses the target KG triple or path together with supporting context triples. We train the Qwen3-14B model using supervised fine-tuning (SFT) under both settings, producing KGModel and CGModel variants. To strengthen the lower-hop factual foundation of the models, we introduce an LLM-judged, history-aware adaptive repair pipeline that identifies unresolved one-hop failures, continually fine-tunes on targeted repair examples, and removes or quarantines problematic noisy triples. This repair stage enables the models to reach 100% accuracy on the cleaned retained one-hop validation sets. Finally, we employ reinforcement learning (RL) using lower-hop question-answer items and evaluate generalization on harder 3-hop, 4-hop, and 5-hop tasks. Across both diseases, context-augmented supervision consistently improves multi-hop performance over KG-only supervision. RL initialized from repaired SFT checkpoints yields larger and more stable gains.

Reasoning benchmarks measure clinical performance on clean inputs. We evaluate the step before reasoning: retrieval over real EHR notes, where negation, temporality, and family-versus-patient attribution can flip a correct answer to a wrong one. EpiKG carries an assertion label and a temporality tag with every fact in a patient knowledge graph, then routes retrieval by question intent. ClinicalBench is a 400-question test over 43 MIMIC-IV patients across 9 assertion-sensitive categories. A 7-condition ablation tests each piece of EpiKG across six LLMs (Claude Opus 4.6, GPT-OSS 20B, MedGemma 27B, Gemma 4 31B, MedGemma 1.5 4B, Qwen 3.5 35B). Three physicians blindly adjudicated 100 paired items. The author-blind primary endpoint, leave-author-out paired exact McNemar on 50 unanimous-strict items rated by two external physicians, yields +22.0 percentage points (95 percent Newcombe CI [+5.1, +31.5], p=0.0192). The architectural novelty, intent-aware KG-RAG over a Contriever dense-RAG baseline (C2b to C4g_kw on the change-excluded n=362 endpoint), is +8.84 percentage points (paired McNemar p=1.79e-3); +12.43 percentage points under oracle intent. Sensitivities agree directionally: three-rater physician majority +24.0 percentage points (subject to single-author circularity); deterministic keyword reproducibility proxy +39.5 percentage points. Across the six models, the gain shrinks as the LLM-alone baseline rises (beta=-1.123, r=-0.921, p=0.009). With n=6 this looks more like regression to the mean than encoding substituting for model size. Physician adjudication identified 56 percent of auto-generated reference answers as defective, a methodological finding indicating that NLP-pipeline clinical-QA benchmarks require physician adjudication to be usable. ClinicalBench, the frozen evaluator, three-rater adjudication data, and the EpiKG output stack are publicly released.