# Learning from Medical Entity Trees: An Entity-Centric Medical Data Engineering Framework for MLLMs

arXiv: https://arxiv.org/abs/2604.25296 · HTML: https://mlsanity.com/paper/2604.25296/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 30 of its 46 references that are in the map.
- First posted on arXiv 28 Apr 2026.

## Builds on (most cited first, 30 of 30)

- [Learning Transferable Visual Models From Natural Language Supervision](https://mlsanity.com/paper/2103.00020/) (2021)
- [Sentence-BERT: Sentence Embeddings using Siamese BERT-Networks](https://mlsanity.com/paper/1908.10084/) (2019)
- [ReAct: Synergizing Reasoning and Acting in Language Models](https://mlsanity.com/paper/2210.03629/) (2022)
- [Visual Instruction Tuning](https://mlsanity.com/paper/2304.08485/) (2023)
- [BLIP-2: Bootstrapping Language-Image Pre-training with Frozen Image Encoders and Large Language Models](https://mlsanity.com/paper/2301.12597/) (2023)
- [GPT-4o System Card](https://mlsanity.com/paper/2410.21276/) (2024)
- [Flamingo: a Visual Language Model for Few-Shot Learning](https://mlsanity.com/paper/2204.14198/) (2022)
- [Qwen2-VL: Enhancing Vision-Language Model's Perception of the World at Any Resolution](https://mlsanity.com/paper/2409.12191/) (2024)
- [Scaling Up Visual and Vision-Language Representation Learning With Noisy Text Supervision](https://mlsanity.com/paper/2102.05918/) (2021)
- [Sigmoid Loss for Language Image Pre-Training](https://mlsanity.com/paper/2303.15343/) (2023)
- [InternVL: Scaling up Vision Foundation Models and Aligning for Generic Visual-Linguistic Tasks](https://mlsanity.com/paper/2312.14238/) (2023)
- [MMMU: A Massive Multi-discipline Multimodal Understanding and Reasoning Benchmark for Expert AGI](https://mlsanity.com/paper/2311.16502/) (2023)
- [Large Language Models Encode Clinical Knowledge](https://mlsanity.com/paper/2212.13138/) (2022)
- [LLaVA-Med: Training a Large Language-and-Vision Assistant for Biomedicine in One Day](https://mlsanity.com/paper/2306.00890/) (2023)
- [BiomedCLIP: a multimodal biomedical foundation model pretrained from fifteen million scientific image-text pairs](https://mlsanity.com/paper/2303.00915/) (2023)
- [PathVQA: 30000+ Questions for Medical Visual Question Answering](https://mlsanity.com/paper/2003.10286/) (2020)
- [SLAKE: A Semantically-Labeled Knowledge-Enhanced Dataset for Medical Visual Question Answering](https://mlsanity.com/paper/2102.09542/) (2021)
- [MedGemma Technical Report](https://mlsanity.com/paper/2507.05201/) (2025)
- [PMC-VQA: Visual Instruction Tuning for Medical Visual Question Answering](https://mlsanity.com/paper/2305.10415/) (2023)
- [Lingshu: A Generalist Foundation Model for Unified Multimodal Medical Understanding and Reasoning](https://mlsanity.com/paper/2506.07044/) (2025)
- [HuatuoGPT, towards Taming Language Model to Be a Doctor](https://mlsanity.com/paper/2305.15075/) (2023)
- [Can AI help in screening Viral and COVID-19 pneumonia?](https://mlsanity.com/paper/2003.13145/) (2020)
- [OmniMedVQA: A New Large-Scale Comprehensive Evaluation Benchmark for Medical LVLM](https://mlsanity.com/paper/2402.09181/) (2024)
- [Fine-grained Late-interaction Multi-modal Retrieval for Retrieval Augmented Visual Question Answering](https://mlsanity.com/paper/2309.17133/) (2023)
- [Derm1M: A Million-scale Vision-Language Dataset Aligned with Clinical Ontology Knowledge for Dermatology](https://mlsanity.com/paper/2503.14911/) (2025)
- [BiMediX2: Bio-Medical EXpert LMM for Diverse Medical Modalities](https://mlsanity.com/paper/2412.07769/) (2024)
- [SDR-Former: A Siamese Dual-Resolution Transformer for Liver Lesion Classification Using 3D Multi-Phase Imaging](https://mlsanity.com/paper/2402.17246/) (2024)
- [Multimodal Large Language Models for Medicine: A Comprehensive Survey](https://mlsanity.com/paper/2504.21051/) (2025)
- [DEEPMED: Building a Medical DeepResearch Agent via Multi-hop Med-Search Data and Turn-Controlled Agentic Training & Inference](https://mlsanity.com/paper/2601.18496/) (2026)
- [MedXIAOHE: A Comprehensive Recipe for Building Medical MLLMs](https://mlsanity.com/paper/2602.12705/) (2026)

## Abstract (arXiv)

Multimodal Large Language Models (MLLMs) have shown transformative potential in medical applications, yet their performance is hindered by conventional data curation strategies that rely on coarse-grained partitioning by modality or department. Such fragmented approaches fail to capture the hierarchical and interconnected nature of clinical medical knowledge, limiting the models' ability to perform fine-grained recognition and complex reasoning. In this paper, we propose a novel Entity-Centric Medical Data Engineering framework. We automatically extract entities from authoritative medical literature to construct a Medical Entity Tree (MET), a hierarchical structure that systematically encodes diseases, anatomical structures, modalities, and symptoms into a unified knowledge repository. Building upon the MET, we propose an advanced data engine that includes: (1) node-guided retrieval to anchor raw data to specific medical concepts, (2) a two-stage hybrid filtering and alignment pipeline to ensure precise visual-semantic correspondence, and (3) knowledge-aware data synthesis to generate enriched captions and targeted reasoning VQA pairs, leveraging structural constraints. Extensive evaluations across six medical benchmarks demonstrate that our approach significantly enhances the medical capabilities of general-purpose MLLMs, improving their ability to handle complex clinical queries and achieve state-of-the-art performance in diverse medical contexts.