Autonomous Knowledge Graph Exploration with Adaptive Breadth-Depth Retrieval

Retrieving evidence for language model queries from knowledge graphs requires balancing broad search across the graph with multi-hop traversal to follow relational links. Similarity-based retrievers provide coverage but remain shallow, whereas traversal-based methods rely on selecting seed nodes to start exploration, which can fail when queries span multiple entities and relations. We introduce ARK: Adaptive Retriever of Knowledge, an agentic KG retriever that gives a language model control over this breadth-depth tradeoff using a two-operation toolset: global lexical search over node descriptors and one-hop neighborhood exploration that composes into multi-hop traversal. ARK alternates between breadth-oriented discovery and depth-oriented expansion without depending on a fragile seed selection, a pre-set hop depth, or requiring retrieval training. ARK adapts tool use to queries, using global search for language-heavy queries and neighborhood exploration for relation-heavy queries. On STaRK, ARK reaches 59.1% average Hit@1 and 67.4 average MRR, improving average Hit@1 by up to 31.4% and average MRR by up to 28.0% over retrieval-based and agentic training-free methods. Finally, we distill ARK's tool-use trajectories from a large teacher into an 8B model via label-free imitation, improving Hit@1 by +7.0, +26.6, and +13.5 absolute points over the base 8B model on AMAZON, MAG, and PRIME datasets, respectively, while retaining up to 98.5% of the teacher's Hit@1 rate.

Graph AI generates neurological hypotheses validated in molecular, organoid, and clinical systems

Neurological diseases are the leading global cause of disability, yet most lack disease-modifying treatments. We present PROTON, a heterogeneous graph transformer that generates testable hypotheses across molecular, organoid, and clinical systems. To evaluate PROTON, we apply it to Parkinson's disease (PD), bipolar disorder (BD), and Alzheimer's disease (AD). In PD, PROTON linked genetic risk loci to genes essential for dopaminergic neuron survival and predicted pesticides toxic to patient-derived neurons, including the insecticide endosulfan, which ranked within the top 1.29% of predictions. In silico screens performed by PROTON reproduced six genome-wide $α$-synuclein experiments, including a split-ubiquitin yeast two-hybrid system (normalized enrichment score [NES] = 2.30, FDR-adjusted $p < 1 \times 10^{-4}$), an ascorbate peroxidase proximity labeling assay (NES = 2.16, FDR $< 1 \times 10^{-4}$), and a high-depth targeted exome sequencing study in 496 synucleinopathy patients (NES = 2.13, FDR $< 1 \times 10^{-4}$). In BD, PROTON predicted calcitriol as a candidate drug that reversed proteomic alterations observed in cortical organoids derived from BD patients. In AD, we evaluated PROTON predictions in health records from $n = 610,524$ patients at Mass General Brigham, confirming that five PROTON-predicted drugs were associated with reduced seven-year dementia risk (minimum hazard ratio = 0.63, 95% CI: 0.53-0.75, $p < 1 \times 10^{-7}$). PROTON generated neurological hypotheses that were evaluated across molecular, organoid, and clinical systems, defining a path for AI-driven discovery in neurological disease.