Daily Papers

While dense biomedical embeddings achieve strong performance, their black-box nature limits their utility in clinical decision-making. Recent question-based interpretable embeddings represent text as binary answers to natural-language questions, but these approaches often rely on heuristic or surface-level contrastive signals and overlook specialized domain knowledge. We propose QIME, an ontology-grounded framework for constructing interpretable medical text embeddings in which each dimension corresponds to a clinically meaningful yes/no question. By conditioning on cluster-specific medical concept signatures, QIME generates semantically atomic questions that capture fine-grained distinctions in biomedical text. Furthermore, QIME supports a training-free embedding construction strategy that eliminates per-question classifier training while further improving performance. Experiments across biomedical semantic similarity, clustering, and retrieval benchmarks show that QIME consistently outperforms prior interpretable embedding methods and substantially narrows the gap to strong black-box biomedical encoders, while providing concise and clinically informative explanations.

This paper presents OG-RAG, an Ontology-Grounded Retrieval Augmented Generation method designed to enhance LLM-generated responses by anchoring retrieval processes in domain-specific ontologies. While LLMs are widely used for tasks like question answering and search, they struggle to adapt to specialized knowledge, such as industrial workflows or knowledge work, without expensive fine-tuning or sub-optimal retrieval methods. Existing retrieval-augmented models, such as RAG, offer improvements but fail to account for structured domain knowledge, leading to suboptimal context generation. Ontologies, which conceptually organize domain knowledge by defining entities and their interrelationships, offer a structured representation to address this gap. OG-RAG constructs a hypergraph representation of domain documents, where each hyperedge encapsulates clusters of factual knowledge grounded using domain-specific ontology. An optimization algorithm then retrieves the minimal set of hyperedges that constructs a precise, conceptually grounded context for the LLM. This method enables efficient retrieval while preserving the complex relationships between entities. OG-RAG applies to domains where fact-based reasoning is essential, particularly in tasks that require workflows or decision-making steps to follow predefined rules and procedures. These include industrial workflows in healthcare, legal, and agricultural sectors, as well as knowledge-driven tasks such as news journalism, investigative research, consulting and more. Our evaluations demonstrate that OG-RAG increases the recall of accurate facts by 55% and improves response correctness by 40% across four different LLMs. Additionally, OG-RAG enables 30% faster attribution of responses to context and boosts fact-based reasoning accuracy by 27% compared to baseline methods.

Developing artificial intelligence (AI) for vertical domains requires a solid data foundation for both training and evaluation. In this work, we introduce TrialPanorama, a large-scale, structured database comprising 1,657,476 clinical trial records aggregated from 15 global sources. The database captures key aspects of trial design and execution, including trial setups, interventions, conditions, biomarkers, and outcomes, and links them to standard biomedical ontologies such as DrugBank and MedDRA. This structured and ontology-grounded design enables TrialPanorama to serve as a unified, extensible resource for a wide range of clinical trial tasks, including trial planning, design, and summarization. To demonstrate its utility, we derive a suite of benchmark tasks directly from the TrialPanorama database. The benchmark spans eight tasks across two categories: three for systematic review (study search, study screening, and evidence summarization) and five for trial design (arm design, eligibility criteria, endpoint selection, sample size estimation, and trial completion assessment). The experiments using five state-of-the-art large language models (LLMs) show that while general-purpose LLMs exhibit some zero-shot capability, their performance is still inadequate for high-stakes clinical trial workflows. We release TrialPanorama database and the benchmark to facilitate further research on AI for clinical trials.

The rapid advancement of transformer-based language models has catalyzed breakthroughs in biomedical and clinical natural language processing; however, plant science remains markedly underserved by such domain-adapted tools. In this work, we present PlantBert, a high-performance, open-source language model specifically tailored for extracting structured knowledge from plant stress-response literature. Built upon the DeBERTa architecture-known for its disentangled attention and robust contextual encoding-PlantBert is fine-tuned on a meticulously curated corpus of expert-annotated abstracts, with a primary focus on lentil (Lens culinaris) responses to diverse abiotic and biotic stressors. Our methodology combines transformer-based modeling with rule-enhanced linguistic post-processing and ontology-grounded entity normalization, enabling PlantBert to capture biologically meaningful relationships with precision and semantic fidelity. The underlying corpus is annotated using a hierarchical schema aligned with the Crop Ontology, encompassing molecular, physiological, biochemical, and agronomic dimensions of plant adaptation. PlantBert exhibits strong generalization capabilities across entity types and demonstrates the feasibility of robust domain adaptation in low-resource scientific fields. By providing a scalable and reproducible framework for high-resolution entity recognition, PlantBert bridges a critical gap in agricultural NLP and paves the way for intelligent, data-driven systems in plant genomics, phenomics, and agronomic knowledge discovery. Our model is publicly released to promote transparency and accelerate cross-disciplinary innovation in computational plant science.

Retrieval-augmented learning based on radiology reports has emerged as a promising direction to improve performance on long-tail medical imaging tasks, such as rare disease detection in chest X-rays. Most existing methods rely on comparing high-dimensional text embeddings from models like CLIP or CXR-BERT, which are often difficult to interpret, computationally expensive, and not well-aligned with the structured nature of medical knowledge. We propose a novel, ontology-driven alternative for comparing radiology report texts based on clinically grounded concepts from the Unified Medical Language System (UMLS). Our method extracts standardised medical entities from free-text reports using an enhanced pipeline built on RadGraph-XL and SapBERT. These entities are linked to UMLS concepts (CUIs), enabling a transparent, interpretable set-based representation of each report. We then define a task-adaptive similarity measure based on a modified and weighted version of the Tversky Index that accounts for synonymy, negation, and hierarchical relationships between medical entities. This allows efficient and semantically meaningful similarity comparisons between reports. We demonstrate that our approach outperforms state-of-the-art embedding-based retrieval methods in a radiograph classification task on MIMIC-CXR, particularly in long-tail settings. Additionally, we use our pipeline to generate ontology-backed disease labels for MIMIC-CXR, offering a valuable new resource for downstream learning tasks. Our work provides more explainable, reliable, and task-specific retrieval strategies in clinical AI systems, especially when interpretability and domain knowledge integration are essential. Our code is available at https://github.com/Felix-012/ontology-concept-distillation

A critical gap exists between the general-purpose visual understanding of state-of-the-art physical AI models and the specialized perceptual demands of structured real-world deployment environments. We present PRISM, a 270K-sample multi-view video supervised fine-tuning (SFT) corpus for embodied vision-language-models (VLMs) in real-world retail environments. PRISM is motivated by a simple observation - physical AI systems fail not because of poor visual recognition, but because they do not understand space, physical dynamics and embodied action well enough to operate reliably in the world. To this end, PRISM is grounded in a novel three-dimensional knowledge ontology that spans spatial knowledge, temporal and physical knowledge, and embodied action knowledge. It covers 20+ capability probes across four evaluation dimensions - Embodied Reasoning (ER), Common Sense (CS), Spatial Perception (SP), and Intuitive Physics (IP), and to our knowledge, PRISM is the first dataset to instantiate all three knowledge dimensions within a single real-world deployment domain. The corpus captures data from egocentric, exocentric and 360° viewpoints across five supermarket locations and includes open-ended, chain-of-thought, and multiple-choice supervision. At 4 fps, PRISM spans approximately 11.8M video frames and approximately 730M tokens, placing it among the largest domain-specific video SFT corpora. Fine-tuning on PRISM reduces the error rate across all 20+ probes by 66.6% over the pre-trained baseline, with significant gains in embodied action understanding where the accuracy improves by 36.4%. Our results suggest that ontology-structured, domain specific SFT can meaningfully strengthen embodied VLMs for real-world settings. The PRISM dataset and more details are available at https://dreamvu.ai/prism

LLMs usually exhibit limitations in their ability to incorporate new knowledge, the generation of hallucinations, and the transparency of their decision-making process. In this paper, we explore how to prompt LLMs with knowledge graphs (KG), working as a remedy to engage LLMs with up-to-date knowledge and elicit the reasoning pathways from LLMs. Specifically, we build a prompting pipeline that endows LLMs with the capability of comprehending KG inputs and inferring with a combined implicit knowledge and the retrieved external knowledge. In addition, we investigate eliciting the mind map on which LLMs perform the reasoning and generate the answers. It is identified that the produced mind map exhibits the reasoning pathways of LLMs grounded on the ontology of knowledge, hence bringing the prospects of probing and gauging LLM inference in production. The experiments on three question & answering datasets also show that MindMap prompting leads to a striking empirical gain. For instance, prompting a GPT-3.5 with MindMap yields an overwhelming performance over GPT-4 consistently. We also demonstrate that with structured facts retrieved from KG, MindMap can outperform a series of prompting-with-document-retrieval methods, benefiting from more accurate, concise, and comprehensive knowledge from KGs. To reproduce our results and extend the framework further, we make our codebase available at https://github.com/wyl.willing/MindMap.

Clinical trial matching is a key process in health delivery and discovery. In practice, it is plagued by overwhelming unstructured data and unscalable manual processing. In this paper, we conduct a systematic study on scaling clinical trial matching using large language models (LLMs), with oncology as the focus area. Our study is grounded in a clinical trial matching system currently in test deployment at a large U.S. health network. Initial findings are promising: out of box, cutting-edge LLMs, such as GPT-4, can already structure elaborate eligibility criteria of clinical trials and extract complex matching logic (e.g., nested AND/OR/NOT). While still far from perfect, LLMs substantially outperform prior strong baselines and may serve as a preliminary solution to help triage patient-trial candidates with humans in the loop. Our study also reveals a few significant growth areas for applying LLMs to end-to-end clinical trial matching, such as context limitation and accuracy, especially in structuring patient information from longitudinal medical records.