OncoTriad-QA: A Patient-Level Radiology-Pathology-Genomics Benchmark for Pan-Cancer Reasoning
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Computer Science > Computation and Language
Title:OncoTriad-QA: A Patient-Level Radiology-Pathology-Genomics Benchmark for Pan-Cancer Reasoning
Abstract:Cancer diagnosis and characterization require integrating complementary evidence from radiology, pathology, genomics, and clinical metadata. However, most medical large language model (LLM) and vision-language model (VLM) benchmarks focus on isolated modalities or narrow image-text tasks, leaving patient-level oncology assessment across multiple evidence streams largely untested. We introduce OncoTriad-QA, a patient-level radiology-pathology-genomics benchmark for pan-cancer question answering. OncoTriad-QA contains 86.1k semantic questions across 9,281 TCGA patient cases from 32 cancer cohorts, aligning CT/MRI radiology, whole-slide histopathology, somatic mutations, copy-number alterations, DNA methylation, bulk RNA-seq, and clinical metadata. Case-specific annotations are constructed through a source-grounded LLM-assisted pipeline using curated labels, diagnostic reports, molecular profiles, and modality-derived evidence as primary sources of truth, with automated consistency checks and clinician review. We also introduce OncoVLM, a reference multimodal model that maps modality-native radiology, pathology, DNA methylation, and RNA-seq evidence into an LLM interface through learned projectors. Experiments show that existing general-purpose and medical LLMs remain limited on comprehensive pan-cancer QA, especially when questions require integrating imaging findings, tumor morphology, and molecular evidence. After fine-tuning on OncoTriad-QA, OncoVLM exceeds MedGemma-4B by an average of 10.7 points when using MCQ accuracy and BERTScore-F1, with consistent gains across multiple-choice and open-ended questions under radiology-only, pathology-only, and all-available settings. These results demonstrate the benchmark's value for training and evaluating models for integrated cancer question answering.
| Subjects: | Computation and Language (cs.CL); Artificial Intelligence (cs.AI) |
| Cite as: | arXiv:2608.02615 [cs.CL] |
| (or arXiv:2608.02615v1 [cs.CL] for this version) | |
| https://doi.org/10.48550/arXiv.2608.02615
arXiv-issued DOI via DataCite
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