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Target selection is crucial in pharmaceutical drug discovery, directly influencing clinical trial success. Despite its importance, drug development remains resource-intensive, often taking over a decade with significant financial costs.…

Quantitative Methods · Quantitative Biology 2024-09-26 David Narganes-Carlon , Anniek Myatt , Mani Mudaliar , Daniel J. Crowther

Zero-shot entity retrieval, aiming to link mentions to candidate entities under the zero-shot setting, is vital for many tasks in Natural Language Processing. Most existing methods represent mentions/entities via the sentence embeddings of…

Computation and Language · Computer Science 2022-11-22 Taiqiang Wu , Xingyu Bai , Weigang Guo , Weijie Liu , Siheng Li , Yujiu Yang

Medical entity retrieval is an integral component for understanding and communicating information across various health systems. Current approaches tend to work well on specific medical domains but generalize poorly to unseen…

Computation and Language · Computer Science 2021-05-27 Luyang Kong , Christopher Winestock , Parminder Bhatia

Knowledge graphs (KGs) play a vital role in enhancing search results and recommendation systems. With the rapid increase in the size of the KGs, they are becoming inaccuracy and incomplete. This problem can be solved by the knowledge graph…

Machine Learning · Computer Science 2024-08-06 Wanxu Wei , Yitong Song , Bin Yao

Retrieval-Augmented Generation (RAG) over Knowledge Graphs (KGs) suffers from the fact that indexing approaches may lose important contextual nuance when text is reduced to triples, thereby degrading performance in downstream…

Computation and Language · Computer Science 2026-03-13 Riccardo Campi , Nicolò Oreste Pinciroli Vago , Mathyas Giudici , Marco Brambilla , Piero Fraternali

Neural IR has advanced through two distinct paths: entity-oriented approaches leveraging knowledge graphs and multi-vector models capturing fine-grained semantics. We introduce QDER, a neural re-ranking model that unifies these approaches…

Information Retrieval · Computer Science 2025-10-14 Shubham Chatterjee , Jeff Dalton

Generative LLMs typically improve Named Entity Recognition (NER) performance through instruction tuning. They excel at generating entities by semantic pattern matching but lack an explicit, verifiable reasoning mechanism. This "cognitive…

Computation and Language · Computer Science 2025-11-18 Hui Huang , Yanping Chen , Ruizhang Huang , Chuan Lin , Yongbin Qin

Named entity recognition on the in-domain supervised and few-shot settings have been extensively discussed in the NLP community and made significant progress. However, cross-domain NER, a more common task in practical scenarios, still poses…

Computation and Language · Computer Science 2024-07-25 Ke Bao , Chonghuan Yang

Zero-shot named entity recognition (NER) is the task of detecting named entities of specific types (such as 'Person' or 'Medicine') without any training examples. Current research increasingly relies on large synthetic datasets,…

Computation and Language · Computer Science 2025-03-10 Jonas Golde , Patrick Haller , Max Ploner , Fabio Barth , Nicolaas Jedema , Alan Akbik

We present NER Retriever, a zero-shot retrieval framework for ad-hoc Named Entity Retrieval, a variant of Named Entity Recognition (NER), where the types of interest are not provided in advance, and a user-defined type description is used…

Information Retrieval · Computer Science 2025-09-05 Or Shachar , Uri Katz , Yoav Goldberg , Oren Glickman

Knowledge graph entity typing (KGET) aims to infer missing entity type instances in knowledge graphs. Previous research has predominantly centered around leveraging contextual information associated with entities, which provides valuable…

Artificial Intelligence · Computer Science 2024-05-24 Zhiwei Hu , Víctor Gutiérrez-Basulto , Zhiliang Xiang , Ru Li , Jeff Z. Pan

Entity alignment (EA) is the task to discover entities referring to the same real-world object from different knowledge graphs (KGs), which is the most crucial step in integrating multi-source KGs. The majority of the existing…

Computation and Language · Computer Science 2021-03-02 Renbo Zhu , Meng Ma , Ping Wang

While large language models (LLMs) show great potential in temporal reasoning, most existing work focuses heavily on enhancing performance, often neglecting the explainable reasoning processes underlying the results. To address this gap, we…

Computation and Language · Computer Science 2025-05-22 Zihao Jiang , Ben Liu , Miao Peng , Wenjie Xu , Yao Xiao , Zhenyan Shan , Min Peng

Multi-hop question answering (MHQA) requires integrating knowledge scattered across multiple passages to derive the correct answer. Traditional retrieval-augmented generation (RAG) methods primarily focus on coarse-grained textual semantic…

Computation and Language · Computer Science 2025-08-18 Changjian Wang , Weihong Deng , Weili Guan , Quan Lu , Ning Jiang

Supervised named entity recognition (NER) in the biomedical domain depends on large sets of annotated texts with the given named entities. The creation of such datasets can be time-consuming and expensive, while extraction of new entities…

Computation and Language · Computer Science 2024-08-27 Miloš Košprdić , Nikola Prodanović , Adela Ljajić , Bojana Bašaragin , Nikola Milošević

Entity resolution (ER) refers to the problem of matching records in one or more relations that refer to the same real-world entity. While supervised machine learning (ML) approaches achieve the state-of-the-art results, they require a large…

Databases · Computer Science 2020-04-07 Renzhi Wu , Sanya Chaba , Saurabh Sawlani , Xu Chu , Saravanan Thirumuruganathan

Given a query and a document corpus, the information retrieval (IR) task is to output a ranked list of relevant documents. Combining large language models (LLMs) with embedding-based retrieval models, recent work shows promising results on…

Computation and Language · Computer Science 2023-11-01 Daman Arora , Anush Kini , Sayak Ray Chowdhury , Nagarajan Natarajan , Gaurav Sinha , Amit Sharma

Recent breakthroughs in single-cell technology have ushered in unparalleled opportunities to decode the molecular intricacy of intricate biological systems, especially those linked to diseases unique to humans. However, these progressions…

Genomics · Quantitative Biology 2025-08-26 Huan Zhao , Yiming Liu , Jina Yao , Ling Xiong , Zexin Zhou , Zixing Zhang

Graph-based Retrieval-Augmented Generation (GraphRAG) enhances LLMs by structuring corpus into graphs to facilitate multi-hop reasoning. While recent lightweight approaches reduce indexing costs by leveraging Named Entity Recognition (NER),…

Artificial Intelligence · Computer Science 2026-04-22 Yifan Song , Xingjian Tao , Zhicheng Yang , Yihong Luo , Jing Tang

Retrieval-Augmented Generation (RAG) struggles with domain-specific enterprise datasets, often isolated behind firewalls and rich in complex, specialized terminology unseen by LLMs during pre-training. Semantic variability across domains…

Computation and Language · Computer Science 2025-08-06 Kunal Sawarkar , Shivam R. Solanki , Abhilasha Mangal
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