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Jan 9

Knowledge-Rich Self-Supervision for Biomedical Entity Linking

Entity linking faces significant challenges such as prolific variations and prevalent ambiguities, especially in high-value domains with myriad entities. Standard classification approaches suffer from the annotation bottleneck and cannot effectively handle unseen entities. Zero-shot entity linking has emerged as a promising direction for generalizing to new entities, but it still requires example gold entity mentions during training and canonical descriptions for all entities, both of which are rarely available outside of Wikipedia. In this paper, we explore Knowledge-RIch Self-Supervision (tt KRISS) for biomedical entity linking, by leveraging readily available domain knowledge. In training, it generates self-supervised mention examples on unlabeled text using a domain ontology and trains a contextual encoder using contrastive learning. For inference, it samples self-supervised mentions as prototypes for each entity and conducts linking by mapping the test mention to the most similar prototype. Our approach can easily incorporate entity descriptions and gold mention labels if available. We conducted extensive experiments on seven standard datasets spanning biomedical literature and clinical notes. Without using any labeled information, our method produces tt KRISSBERT, a universal entity linker for four million UMLS entities that attains new state of the art, outperforming prior self-supervised methods by as much as 20 absolute points in accuracy.

  • 9 authors
·
Dec 15, 2021

Reverse Region-to-Entity Annotation for Pixel-Level Visual Entity Linking

Visual Entity Linking (VEL) is a crucial task for achieving fine-grained visual understanding, matching objects within images (visual mentions) to entities in a knowledge base. Previous VEL tasks rely on textual inputs, but writing queries for complex scenes can be challenging. Visual inputs like clicks or bounding boxes offer a more convenient alternative. Therefore, we propose a new task, Pixel-Level Visual Entity Linking (PL-VEL), which uses pixel masks from visual inputs to refer to objects, supplementing reference methods for VEL. To facilitate research on this task, we have constructed the MaskOVEN-Wiki dataset through an entirely automatic reverse region-entity annotation framework. This dataset contains over 5 million annotations aligning pixel-level regions with entity-level labels, which will advance visual understanding towards fine-grained. Moreover, as pixel masks correspond to semantic regions in an image, we enhance previous patch-interacted attention with region-interacted attention by a visual semantic tokenization approach. Manual evaluation results indicate that the reverse annotation framework achieved a 94.8% annotation success rate. Experimental results show that models trained on this dataset improved accuracy by 18 points compared to zero-shot models. Additionally, the semantic tokenization method achieved a 5-point accuracy improvement over the trained baseline.

  • 9 authors
·
Dec 18, 2024

LEMONADE: A Large Multilingual Expert-Annotated Abstractive Event Dataset for the Real World

This paper presents LEMONADE, a large-scale conflict event dataset comprising 39,786 events across 20 languages and 171 countries, with extensive coverage of region-specific entities. LEMONADE is based on a partially reannotated subset of the Armed Conflict Location & Event Data (ACLED), which has documented global conflict events for over a decade. To address the challenge of aggregating multilingual sources for global event analysis, we introduce abstractive event extraction (AEE) and its subtask, abstractive entity linking (AEL). Unlike conventional span-based event extraction, our approach detects event arguments and entities through holistic document understanding and normalizes them across the multilingual dataset. We evaluate various large language models (LLMs) on these tasks, adapt existing zero-shot event extraction systems, and benchmark supervised models. Additionally, we introduce ZEST, a novel zero-shot retrieval-based system for AEL. Our best zero-shot system achieves an end-to-end F1 score of 58.3%, with LLMs outperforming specialized event extraction models such as GoLLIE. For entity linking, ZEST achieves an F1 score of 45.7%, significantly surpassing OneNet, a state-of-the-art zero-shot baseline that achieves only 23.7%. However, these zero-shot results lag behind the best supervised systems by 20.1% and 37.0% in the end-to-end and AEL tasks, respectively, highlighting the need for further research.

  • 9 authors
·
Jun 1, 2025

CM3: A Causal Masked Multimodal Model of the Internet

We introduce CM3, a family of causally masked generative models trained over a large corpus of structured multi-modal documents that can contain both text and image tokens. Our new causally masked approach generates tokens left to right while also masking out a small number of long token spans that are generated at the end of the string, instead of their original positions. The casual masking object provides a type of hybrid of the more common causal and masked language models, by enabling full generative modeling while also providing bidirectional context when generating the masked spans. We train causally masked language-image models on large-scale web and Wikipedia articles, where each document contains all of the text, hypertext markup, hyperlinks, and image tokens (from a VQVAE-GAN), provided in the order they appear in the original HTML source (before masking). The resulting CM3 models can generate rich structured, multi-modal outputs while conditioning on arbitrary masked document contexts, and thereby implicitly learn a wide range of text, image, and cross modal tasks. They can be prompted to recover, in a zero-shot fashion, the functionality of models such as DALL-E, GENRE, and HTLM. We set the new state-of-the-art in zero-shot summarization, entity linking, and entity disambiguation while maintaining competitive performance in the fine-tuning setting. We can generate images unconditionally, conditioned on text (like DALL-E) and do captioning all in a zero-shot setting with a single model.

  • 11 authors
·
Jan 19, 2022