BEACON-SP: Ontology-Grounded GraphRAG Framework for Clinical Suicide Risk Assessment

Explainable suicide-risk assessment requires models not only to estimate risk severity, but also to identify supporting language and the risk and protective factors expressed in a post. We present our system for the IEEE BigData 2026 Cup on Explainable Suicide Risk Assessment on Social Media, which addresses three tasks: risk-level classification, evidence phrase extraction, and multi-label factor identification. Our approach adapts Qwen2.5-Instruct models using quantized low-rank adaptation (QLoRA) and an answer-masked causal language-model objective. We jointly train across all three tasks for risk classification, jointly train on Tasks1a and 1b for evidence extraction, and adapt Task2 separately for factor identification. We also tailor aggregation to each output: we average risk-level probabilities from the 32B and 72B models, combine evidence phrases through cross-fold consensus, and calibrate factor-specific decisions through rate matching based on out-of-fold operating points. On the official leaderboard, the final system achieved a composite score of 0.7738, with 0.8089 on Task1 and 0.6919 on Task2. Across the evaluated configurations, three-task training performed best for Task1a, joint training on Tasks1a and 1b performed best for Task1b, and task-specific training performed best for Task2. Probability averaging further improved Task~1a when component models had complementary errors. These findings highlight the value of tailoring both training objectives and aggregation strategies to the output structure of each task within a unified language-model framework.

Assessing suicide risk from social media text is a small-data, high-stakes setting requiring not only severity prediction but also supporting evidence and clinically relevant risk and protective factors. Yet common NLP techniques, including model scaling, synthetic data, loss reweighting, ensembling, and threshold tuning, are often applied without testing whether their gains hold up under severe class imbalance, coupled outputs, and limited author-level data. We study 1,635 clinician-annotated posts and audit 31 pre-specified techniques from 7 methodological families through roughly 300 controlled experiments on author-disjoint partitions. We found no prior audit of this playbook in this regime. The findings guide a task-grounded system for three outputs: 4-level suicide risk, evidence spans, and 24 clinical risk and protective factors. Only 5 of 31 comparisons produced reliable gains. We reformulate factor prediction as entailment between each post and its codebook definitions, using an architecturally diverse ensemble with class-balanced training and score rescaling. Risk predictions condition a 7-model evidence tagger ensemble; evidence restricts symbolic risk rules; and a difficult risk class is routed separately. The factor predictor remains independent because risk evidence provides no additional factor signal. We also correct a mismatch between validation scores used for threshold fitting and test-time ensemble scores through deployment-consistent calibration, yielding the largest improvement to the factor system. The final system achieves 0.8203 for risk, 0.7953 for evidence, and 0.7045 macro-F1 for factors, with a 0.7781 composite, ranking third among 53 teams. We call the underlying principle task-conditioned technique selection: retain techniques only when task-specific knowledge, structure, or empirical evidence justifies them.

Biomedical knowledge graphs (KGs) treat disease associations as static facts, but temporal information is crucial for clinical reasoning, e.g., a symptom diagnostic of one disease at age 3 may imply a different disease at age 13. Existing KGs such as PrimeKG, Hetionet, and iKraph do not encode when a finding becomes clinically relevant over the course of a disease. This limits their usefulness for longitudinal clinical reasoning and retrieval augmentation. We introduce ChronoMedKG, a temporal biomedical knowledge graph that contains 460,497 evidence-linked triples (filtered from 13M raw extractions) covering 13,431 diseases. Each association is tied to temporal components like onset window or progression stage, which are backed by PMID-traceable evidence and a multi-signal credibility score. The graph is constructed through a disease-autonomous multi-agent pipeline in which multiple frontier LLMs independently extract knowledge from PubMed and PMC literature. Only those relations are kept that are supported by multi-model consensus, survive credibility filtering, as well as ontology alignment. ChronoMedKG scored 92.7% agreement against Orphadata and adds temporal grounding for 6,250 diseases absent from HPOA, Orphadata, and Phenopackets, including 1,657 Orphanet-coded rare diseases. We further introduce ChronoTQA, a benchmark of 3,341 questions across eight task types (six temporal plus two static controls), with a 12-question supplementary probe. Frontier LLMs lose roughly 30 points moving from static to temporal questions; ChronoMedKG retrieval rescues 47-65% of their long-tail failures, against 17-29% for HPOA-RAG. As such, ChronoMedKG provides a crucial temporal axis for retrieval-augmented clinical systems that was previously absent.