Knowledge Graph-Driven Expert-Level Reasoning for Neuroscience
Authors: Jake Stephen, Niraj K. Jha
Organizations: Department of Electrical and Computer Engineering, Princeton University
Abstract
Knowledge graph (KG) is an abstraction that can be extracted from text corpora and used for in-depth reasoning. Prior work has leveraged KGs to fine-tune language models (LMs), enabling domain-specific superintelligence. In this work, we explore whether KG-driven in-depth reasoning capabilities can emerge in neuroscience using only information contained within a single authoritative textbook. The central hypothesis is that structured knowledge, when distilled into a high-quality KG and converted into KG-grounded question-answer (QA) supervision, is sufficient to produce expert-level reasoning through a fine-tuned LM that surpasses large language models (LLMs) in accuracy, while employing orders of magnitude fewer parameters. We construct a textbook-derived KG via a dual-LLM validation pipeline, expand it with a masked LM trained on the KG topology, generate multi-hop QA items, which include QA pairs and reasoning traces, to fine-tune an LM exclusively on KG-derived supervision, and apply reinforcement learning using path-derived KG signals as implicit reward models. Our results demonstrate that deep, mechanistic neuroscience understanding can be induced in the model without reliance on large, heterogeneous web-scale corpora. The KG-based synthetic neuroscience curriculum that readers can quiz themselves on, and the fine-tuned LM, are available at the following GitHub location: https://kg-bottom-up-superintelligence.github.io/neuro-bench.
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.
Knowledge Graphs (KGs) are widely used to mitigate the limitations of Large Language Models (LLMs), such as outdated knowledge and hallucinations. Existing LLM-KG integration frameworks typically rely on predefined operators to retrieve factual knowledge from KGs and inject it into prompts for answer generation. This paradigm faces two critical bottlenecks: 1) Inflexibility: The predefined operators are limited in scope and thus lack sufficient compositional expressiveness to fully capture the complex semantics required by KG questions. 2) Unscalability: Direct injection of factual knowledge into prompts limits scalability in handling large-scale factual knowledge. To address these two bottlenecks, we propose Code-on-Graph (CoG), a programmatic reasoning framework for LLM-KG integration. Specifically, given the factual knowledge retrieved at each reasoning step, CoG first identifies the corresponding KG schemas and represents these schemas as Python classes, which serve as abstract interfaces to the retrieved facts. It then generates executable code grounded in these classes, with the retrieved facts instantiated as objects of the corresponding classes during execution. This design enables flexible code-based reasoning while avoiding the direct injection of large-scale factual knowledge into prompts. Experiments on WebQSP, CWQ, and GrailQA demonstrate that CoG outperforms prior state-of-the-art models by up to 10.5%.
Modern Large Language Models (LLMs) have shown impressive performances in user-facing tasks such as question answering, as well as consistent improvements in reasoning capabilities. Still, the way these models encode knowledge seems inherently flawed: by design, LLMs encode world-knowledge within their parameters. This way of representing knowledge is inherently opaque, difficult to debug and update, and prone to hallucinations. On the other hand, Knowledge Graphs can provide human-readable and easily editable world knowledge representations, and their application in knowledge-intensive tasks has consistently proven beneficial to downstream performance. Nonetheless, current integration techniques require extensive retraining or finetuning. To overcome this issue, we introduce KoRe, a methodology to encode 1-hop sub-graphs into compact discrete knowledge tokens and inject them into a LLM backbone. We test the proposed approach on three established benchmarks, and report competitive performances coupled with a significant reduction (up to 10x) in token usage. Our results show that compact discrete KG representations can efficiently and effectively be used to ground modern LLMs.