The paper introduces a unified framework for aligning biomedical text with knowledge graphs using a lightweight projection learned via contrastive learning, keeping the text encoder and KG embedding model frozen. It evaluates six design choices—text encoder, KG embedding, projection head, triple composition, training direction, and hard‑negative sampling—on a newly created CTD‑Align corpus of 22K chemical‑gene interaction pairs linked to PubMed passages. The study finds that triple composition and training direction have the largest impact, while simpler linear projections over concatenated subject, predicate, and object embeddings yield the best performance.
arXiv:2511.21075v4 Announce Type: replace-cross Abstract: Engineering LLMs to accelerate life sciences research requires a robust alignment with biomedical knowledge. We observe that biomedical text...
EvidenceNet is a disease‑specific dataset that transforms full‑text biomedical literature into structured evidence records and graph representations, preserving study design, provenance, and quantitative support. Using an LLM‑assisted pipeline, it extracts experimentally grounded findings, normalizes entities, scores evidence quality, and links related records via typed semantic relations. The released subsets—EvidenceNet‑HCC and EvidenceNet‑CRC—contain thousands of evidence records and richly connected graphs, with high extraction and relation‑type accuracy, enabling retrieval‑augmented question answering and graph‑based tasks such as link prediction and target prioritization.
OptimusKG is a multimodal biomedical labeled property graph that integrates structured and semi‑structured resources to preserve detailed, type‑specific metadata across molecular, anatomical, clinical, and environmental domains. The graph contains nearly 191,000 nodes, over 21.8 million edges, and more than 67 million property instances derived from 18 ontologies, with a top‑level schema that enforces node and edge constraints while retaining granular provenance. Validation using the PaperQA3 agent found that 70.0% of sampled edges are supported by literature evidence, and the graph offers a standardized resource for machine learning, knowledge‑grounded retrieval, and hypothesis generation in biomedical research.
arXiv:2608. 03855v1 Announce Type: new Abstract: Transformer models have revolutionized natural language processing (NLP), and text-based molecular representations like SMILES have successfully extended these architectures to chemistry.
arXiv:2608. 16005v1 Announce Type: new Abstract: This paper studies the problem of molecule-text alignment, which aims to project molecules and their textual descriptions into a joint latent space for downstream tasks including molecule search and molecular property prediction.
The paper introduces Distilled Rapid Embedding Transfer (DRET), a parameter‑efficient method that injects biomedical domain knowledge from large specialized models into a smaller general‑purpose model without retraining on the original specialized corpora. DRET evolves through iterative strategies—tokenizer‑merge (DRET 1.x), hybrid embedding averaging (DRET 2.0), priority‑based embedding transfer (DRET 3.x), and further refinements (DRET 4.x)—and demonstrates that a 66‑million‑parameter DistilBERT can achieve competitive or superior performance on token‑level PICO classification compared to much larger models, while remaining lightweight. The authors validate the embedding‑level transfer with cosine similarity, semantic‑shift, and t‑SNE analyses, highlighting DRET’s potential for scalable, resource‑efficient biomedical text mining.
arXiv:2608.24121v1 Announce Type: new Abstract: Radiology report generation (RRG) has recently benefited from large language models, which substantially improve report fluency. However, clinically fa...
The study investigates how document segmentation and chunk representation affect retrieval-augmented generation (RAG) for chemistry texts. Using the ChemQuests corpus, the authors benchmark 41 embedding models and evaluate them across five chunking strategies, seven chunk sizes, and various overlap settings. They find that embedding choice has the largest impact, with models like E5, BGE, and Nomic performing best, and recommend medium-to-large chunks with fixed-token, recursive-token, or hierarchical-section chunking and low overlap for effective chemistry-aware RAG.
The study investigates how post‑training alignment techniques affect small language models (SLMs) for generating medication leaflets from structured biomedical data. Four alignment methods—supervised fine‑tuning (SFT), direct preference optimization (DPO), odds ratio preference optimization (ORPO), and group relative policy optimization (GRPO)—are evaluated using Qwen‑2.5 models, with a new FDALeaflets dataset derived from OpenFDA drug labels for zero‑shot cross‑regulatory testing. Results show that aligned SLMs can outperform GPT‑5 on reference‑based metrics, while ORPO and GRPO achieve the highest semantic textual similarity scores in‑domain and on FDALeaflets, respectively, highlighting the importance of alignment for semantic fidelity and generalization.
arXiv:2606. 06109v1 Announce Type: cross Abstract: Entity alignment (EA) aims to identify equivalent entities across heterogeneous knowledge graphs (KGs) and is a key component of knowledge fusion and cross-KG reasoning.
arXiv:2608. 19201v1 Announce Type: cross Abstract: Bioinformatics software and databases are essential components of modern life science research, yet their mentions in the scientific literature are often inconsistent and difficult to systematically identify at scale.
arXiv:2609.21164v1 Announce Type: new Abstract: Integrating diverse data modalities --- such as clinical notes, laboratory results, and medical imaging --- is essential for advancing clinical decisio...