21 papers · ranked by Valyu relevance
Zhuoling Li, Ha Linh Hong Tran Nguyen, Valeria Bladinieres, Maxim Romanovsky
Graph-based Retrieval-Augmented Generation (GraphRAG) extends traditional RAG by using knowledge graphs (KGs) to give large language models (LLMs) a structured, semantically coherent context, yielding more grounded answers. However, GraphRAG reasoning process remains a black-box, limiting our ability to understand how…
Edmund Evangelista, Fathima Ruba, Salman Bukhari, Amril Nazir + 2 more
Background Gestational diabetes mellitus (GDM) is a prevalent chronic condition that affects maternal and fetal health outcomes worldwide, increasingly in underserved populations. While generative artificial intelligence (AI) and large language models (LLMs) have shown promise in health care, their application in GDM…
Ruichen Zhang, Feda AlMuhisen, Chenguang Wan, Zhisong Qu + 5 more
Accurate parameter selection is fundamental to gyrokinetic plasma simulations, yet current practices rely heavily on manual literature reviews, leading to inefficiencies and inconsistencies. We introduce Plasma GraphRAG, a novel framework that integrates Graph Retrieval-Augmented Generation (GraphRAG) with large…
Xin He, Yili Wang, Wenqi Fan, Qing Li + 3 more
Question answering (QA) over complex documents requires models to retrieve and integrate evidence distributed across distant document regions and modalities. Multimodal GraphRAG provides a promising direction by organizing document evidence with graph structures. However, existing methods often suffer from unreliable…
Shuhua Yang, Jiahao Zhang, Yilong Wang, Dongwon Lee + 1 more
Graph-based retrieval-augmented generation (GraphRAG) systems construct knowledge graphs over document collections to support multi-hop reasoning. While prior work shows that GraphRAG responses may leak retrieved subgraphs, the feasibility of query-efficient reconstruction of the hidden graph structure remains…
Hao Wu, Nengfu Xie, Xiaoli Wang, Jingchao Fan + 2 more
Intelligent prevention and control of crop diseases and pests is a critical link in safeguarding food security. However, agricultural practitioners often face fragmented information and low retrieval efficiency when seeking accurate, actionable knowledge. Furthermore, general-purpose large language models (LLMs) are…
Jie Song, Jinhua Feng, Yuxin Zhang, Cheng Bi + 12 more
Personalized perioperative fluid therapy is important for reducing postoperative complications and adverse outcomes. Although large language models (LLMs) show promise in healthcare, their application in fluid therapy remains challenged by hallucinations, limited domain-specific knowledge, and insufficient…
W.Y. Wang, Peizhuo Lv, Yan Wang, Rujie Dai + 6 more
—Graph Retrieval-Augmented Generation (GraphRAG) has emerged as a key technique for enhancing Large Language Models (LLMs) with proprietary Knowledge Graphs (KGs) in knowledge-intensive applications. As these KGs often represent an organization's highly valuable intellectual property (IP), they face a significant risk…
Shanghao Li, Jinda Han, Yibo Wang, Yuanjie Zhu + 4 more
Graph-based Retrieval-Augmented Generation (GraphRAG) enhances Large Language Models (LLMs) by incorporating external knowledge from linearized subgraphs retrieved from knowledge graphs. However, LLMs struggle to interpret the relational and topological information in these inputs, resulting in hallucinations that are…
Herbert George, Gowtham Baratam, DS Dhyaneesh
Drug repurposing has become a crucial strategy to accelerate drug discovery and reduce development costs. Conventional drug development is time consuming and expensive; it often takes more than a decade and billions of dollars to bring a new drug into the market. To address these challenges, this work puts forward a…
Sebastien Ravel, Nina Marthe, Camille Carrette, Mourdas Mohamed + 2 more
Pangenome variation graphs (PVGs), which represent genomic diversity through multiple genomes alignment, are powerful tools for studying genomic variations in populations. However, current tools often lack integration, efficiency, or require format conversions, to use them, hindering their usability. Here, we introduce…
Yuhan Zhao, Yiqun Miao, Rongrong Guo, Yuan Luo + 3 more
Background Inference-time retrieval augmentation is increasingly used to improve the traceability and verifiability of large language model (LLM) applications in health care. Evaluation practices for text-based retrieval-augmented generation (RAG) and graph-structured RAG (GraphRAG) systems remain heterogeneous, which…
Authors not listed
Pharmacophores are widely used to describe protein-ligand interactions, and the Grids of Pharmacophore Interaction Fields (GRAIL) method extends this concept by representing binding pockets as interpretable sets of interaction type-specific pharmacophoric maps. In this work, we propose a hybrid framework for binding…
Nicole Bergen, Katherine Kirkby, Devaki Nambiar, Anne Schlotheuber + 1 more
Several resources and tools have been developed for carrying out health inequality analysis, including the preparation of disaggregated data and calculation of summary measures of health inequality. There is also a body of literature that addresses best practices for the preparation of commonly used graphs and maps.…
Authors not listed
We present graphRC, a graph-based method for rapid transition state (TS) mode analysis that provides chemical insight along normal mode displacements and reaction coordinate trajectories by translating Cartesian displacements into meaningful internal coordinate changes. Internal coordinates are constructed using…
Authors not listed
Topological band theory based on the variety of reciprocal space invariants provides an insightful framework for quantum material characterization in condensed matter physics. Its bulk-boundary correspondence principle has become a reliable tool for predicting Fermi level properties. Here, we investigate a recently…
Martin Schmitz, Leon Rauschning, Kenji Kawaguchi, Mile Sikic
Accurate haplotype phasing is essential for high-quality genome assembly, yet de novo phasing of complex genomes without parental data remains challenging. We formulate haplotype phasing as a node clustering problem with overlapping clusters on augmented unitig graphs, where nodes represent contiguous, non-branching…
Authors not listed
Finding the most stable adsorption geometry of a flexible molecule on a catalytic surface remains a key challenge due to the high dimensionality and ruggedness of the potential energy surface. We present a Gradient-Enhanced Genetic Algorithm (GE-GA) for the global optimization of adsorbate–surface configurations…
Hargobinder Kaur, Rebekah B. Guevara, Yolanda Rivera-Cuevas, Einar B. Olafsson + 9 more
The endosomal sorting complex required for transport (ESCRT) is a hetero-multimeric membrane-remodeling machinery essential for endosomal sorting, intraluminal vesicle formation, cytokinetic abscission, and membrane repair. ESCRT is also hijacked by some pathogens including the protozoan Toxoplasma gondii, which…
Authors not listed
LC-HRMS is widely used in forensic toxicology for broad-scope screening. When a newly emerging or rarely encountered compound is tentatively identified, toxicologists must decide whether it may be relevant to the case and, if so, quantify it. Acquiring reference material for quantification is costly and time-consuming.…
Anna Lisiecka, Agnieszka Kowalewska, Norbert Dojer
Pangenome graphs conveniently represent genetic variation within a population. Several types of such graphs have been proposed, with varying properties and potential applications. Among them, variation graphs (VGs) seem best suited to replace reference genomes in sequencing data processing, while whole genome…